diff --git a/myst.yml b/myst.yml new file mode 100644 index 0000000000..1775c8c065 --- /dev/null +++ b/myst.yml @@ -0,0 +1,21 @@ +# See docs at: https://mystmd.org/guide/frontmatter +version: 1 +project: + id: 9ec8e89f-ba6d-471e-a169-ca19a0680df2 + # title: + # description: + keywords: [] + authors: [] + github: https://github.com/tahiri-lab/scipy_proceedings_2024 + # bibliography: [] +site: + template: book-theme + # title: + # options: + # favicon: favicon.ico + # logo: site_logo.png + nav: [] + actions: + - title: Learn More + url: https://mystmd.org/guide + domains: [] diff --git a/papers/Gagnon_Keke_Tahiri_2024/banner.png b/papers/Gagnon_Keke_Tahiri_2024/banner.png new file mode 100644 index 0000000000..c5dd028e26 Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/banner.png differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/figure1.png b/papers/Gagnon_Keke_Tahiri_2024/figure1.png new file mode 100644 index 0000000000..cd768ee933 Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/figure1.png differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/figure2.png b/papers/Gagnon_Keke_Tahiri_2024/figure2.png new file mode 100644 index 0000000000..2ff94d5a6b Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/figure2.png differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/figure3.avif b/papers/Gagnon_Keke_Tahiri_2024/figure3.avif new file mode 100644 index 0000000000..c11dbd9275 Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/figure3.avif differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/figure4.png b/papers/Gagnon_Keke_Tahiri_2024/figure4.png new file mode 100644 index 0000000000..2f2b61fd98 Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/figure4.png differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/figure5.webp b/papers/Gagnon_Keke_Tahiri_2024/figure5.webp new file mode 100644 index 0000000000..d1ccbd70b2 Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/figure5.webp differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/figure6.png b/papers/Gagnon_Keke_Tahiri_2024/figure6.png new file mode 100644 index 0000000000..906554ed33 Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/figure6.png differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/figure7.webp b/papers/Gagnon_Keke_Tahiri_2024/figure7.webp new file mode 100644 index 0000000000..11f76cc299 Binary files /dev/null and b/papers/Gagnon_Keke_Tahiri_2024/figure7.webp differ diff --git a/papers/Gagnon_Keke_Tahiri_2024/main.tex b/papers/Gagnon_Keke_Tahiri_2024/main.tex new file mode 100644 index 0000000000..cd443a2587 --- /dev/null +++ b/papers/Gagnon_Keke_Tahiri_2024/main.tex @@ -0,0 +1,116 @@ +\begin{abstract} +Climate change and various anthropogenic factors significantly influence biodiversity and population evolutionary dynamics. To deepen our understanding of the mechanisms driving these disturbances within ecosystems, biologists employ phylogeographic approaches. These methods aim to establish the correlation between the genetic structure of populations and their geographical distribution, considering their current or historical geoclimatic history. + +Our laboratory focuses on developing bioinformatics tools to enhance phylogeographic analysis. Recognizing the urgency of the current climate crisis, we are conducting an in-depth analysis of the impact of extreme climatic parameters and environmental factors on Cumacea (crustaceans: Peracarida). Our approach includes a comparative study that validates our phylogeographic models against environmental data from the northern waters of the North Atlantic around Iceland. Concurrently, we are updating a Python package (in beta) to facilitate these complex analyses. +\end{abstract} + +\section{Introduction}\label{introduction} +In the vast North Atlantic and subarctic region, the Icelandic region and its surrounding waters offer fascinating ecological interest \citep{brix_iceage_2014, hansen_north_2000, schnurr_composition_2014, uhlir_adding_2021}. The waters surrounding Iceland contains a significant diversity of water bodies from various sources \citep{brix_iceage_2014, uhlir_adding_2021} often interacting and frequently overlapping \citep{malmberg_hydrographic_2003, brix_distribution_2010, meisner_benthic_2014, uhlir_adding_2021}. These specific oceanographic and hydrographic caracteristics shape benthic habitats through depth gradients, water mass indicators, and a particular arrangement of habitats \citep{meisner_benthic_2014, uhlir_adding_2021}. Therefore, research in these areas enhances our understanding of the deep-sea ecosystems and the patterns of biodiversity found witnin them \citep{meisner_prefacebiodiversity_2018, uhlir_adding_2021}. + +Biological and environmental baseline data collected in these regions by the IceAGE project, as well as its predecessors, BIOFAR (Biology of the Faroe Island; \citep{norrevang_list_1994, gerken_cumacea_1999}) and BIOICE (Benthic Invertebrates of Icelandic waters; \citep{omarsdottir_biodiversity_2013}), which studied the biodiversity of the Faroe Islands and Iceland \citep{meisner_prefacebiodiversity_2018}, are an invaluable resource. They provide crucial source of information for understanding two major issues facing present and future generations: the impact of climate change and mining on the seabed. The North Atlantic region around Iceland has been recongnized for decades as a crucial region for the regulation of global thermohaline circulation \citep{meisner_prefacebiodiversity_2018}. The Greenland, Iceland, and Norwegian (GIN) seas, as well as the high-latitude North Atlantic, play a crucial role in modern deep-sea ventilation. The surface waters of this region are vital for the global deep-sea renewal as well as important for the circulation of thermohaline \citep{johannessen_relationship_1994}. One of the most important changes is the formation of cold, deep water \citep{winton_effect_1997, lohmann_sea_1998, meehl_global_2007, meisner_prefacebiodiversity_2018}. With the loss of Arctic sea ice, the deep-sea formation process slowed down, likely impacting flow and chemistry in the region studied during the IceAGE expedition \citep{meisner_prefacebiodiversity_2018}. + +There is growing international interest in deep-sea resource extraction, and mining operations are about to begin in some areas \citep{nath_environment_2000, halfar_danger_2007, mengerink_call_2014}. These operations target in particular mid-ocean ridges and other active geothermal areas. The ridges around Iceland include such areas, such as Reykjanes Ridge, which is home to hydrothermal vent sites. Accurately and rigorously assessing the extent of damage and loss of ecosystem services caused by mining activities is difficult without robust baseline data \citep{meisner_prefacebiodiversity_2018}. + +Crustaceans of the taxon Peracarida Calman, 1904, often constitute a significant portion of macrobenthic communities in Arctic and subarctic waters \citep{brandt_biodiversity_1997, conlan_distribution_2008, stransky_diversity_2010, uhlir_adding_2021} and can be widely dispersed over the continental shelf and slope of the northern seas \citep{hansen_crustacea_1916, just_amphipoda_1980, svavarsson_distribution_1990, svavarsson_deep-sea_1993, brandt_peracarid_1995, brandt_species_1996, uhlir_adding_2021}. In this study, we focus on the peracarid taxon Cumacea Krøyer, 1846. The latter are mainly bottom-dwelling marine benthic crustaceans, spending a large part of their lives buried in or near sediments \citep{uhlir_adding_2021}. Thus, Cumacea are presumed to have limited dispersal abilities and are unlikely to be able to move great distances \citep{rex_community_1981, wilson_speciation_1987, uhlir_adding_2021}. + +Unlike the benthic invertebrates that inhabit rocky intertidal environments of the Northwest and Northeast Atlantic \citep{wares_community_2002, maggs_evaluating_2008, ilves_colonization_2010, jennings_phylogeographic_2014}, the available information on the evolutionary history and dynamics of deep-sea benthic invertebrates in the North Atlantic remains limited \citep{etter_phylogeography_2011, jennings_phylogeographic_2014}. A homogenous genetic structure with the expansion of North Atlantic populations farther towards the poles has been detected (e.g., \citep{aarbakke_discovery_2011}), emphasizing the role and importance of considering climate change in range expansion \citep{jennings_phylogeographic_2014}. Although studies reveal interesting patterns of genetic distribution of benthic invertabrates from the deep-sea (e.g., \citep{wilson_historical_1998, havermans_genetic_2013, jennings_phylogeographic_2014}), it's fundamental to better understand the origin and demography of deep Atlantic biota in order to deepen our understading of their contemporary connectivity in an evolutionary context as well as to grasp their relationship with ongoing climate change. Continued warming opens up transarctic routes \citep{jennings_phylogeographic_2014}. + +In the context of the current climate emergency, this study aims to undertake an in-depth analysis of the influence of extreme climatic parameters and environmental peculiarities on Cumacea (crustaceans: Peracarida). Thus, we wish to determine if there is a correlation between the genetic information of regions of the mitochondrial 16S rRNA gene of these species and the physical characteristics of their habitats. Our approach includes a comparative study to validate our different phylogeographic models by comparing them to the environmental factors found in the waters of the North Atlantic around Iceland. At the same time, we will be updating a Python package (in beta) to facilitate these complex analyses. + +\section{Related Works}\label{related-works} +Many studies have investigated the relationship between genetics and the climatic conditions of their study region. These studies have provided a better understanding of how organisms adapt to their habitat and evolve in it over time \citep{ghalambor_adaptive_2007, linnen_measuring_2009, schluter_evidence_2009, barrett_molecular_2011, fc_genomic_2012}. They have also helped develop conservation plans to maintain biodiversity and protect endangered species by designing how populations are adapted to their environment \citep{frankham_introduction_2002, reed_correlation_2003, tallmon_alluring_2004, holderegger_brief_2006, balkenhol_identifying_2009}. + +\cite{koshkarov_phylogeography_2022} proposed a phylogeographic approach based on an algorithm called aPhyloGeo to study the correlation between SARS-COV-2 variants and their geographical characteristics. More recently, \cite{li_aphylogeo-covid_2023} have developed an interactive platform called aPhyloGeo-Covid to facilitate these analyses. We elaborate on the aPhyloGeo software as well as its use in this study later in this article. + +A study by \cite{ghalambor_adaptive_2007} has demonstrated that habitat characteristics, such as water temperature, can affect the genetics of guppy populations (Poecilla reticulata) by shaping their phenotypic plasticity as well as by promoting rapid genetic adaptation. \cite{cheviron_genomic_2012} also concluded that there was a correlation between vertebrate genetics and habitat properties, particularly in extreme environments such as high altitudes. This correlation between genetics and environmental characteristics was also supported by the results of studies of Threespine Sticklebacks \citep{colosimo_widespread_2005, fc_genomic_2012}. Those results aren't suprinsing consider that species acclimatization to climate change is often the result of the interaction between genetic variation among populations and selection pressures caused by environmental changes \citep{hoffmann_climate_2011}. + +However, studies have highlighted the complexity of the relationships between genetics and the environment that can be influenced by many factors such as genotype-environment interaction and natural selection. This can make it difficult to identify unambiguous causal relationships between these two parameters \citep{manel_landscape_2003, holderegger_brief_2006, storfer_putting_2007, balkenhol_identifying_2009, manel_perspectives_2010}. Other studies mention that it is difficult to distinguish between the direct and indirect effects of the environment on genetics \citep{luikart_power_2003, holderegger_brief_2006, balkenhol_identifying_2009, manel_perspectives_2010, balkenhol_landscape_2019}. Studies of the effect of the environment on the genetics of organisms may be limited by the methods available to measure genetic and environmental characteristics, as well as by logistical constraints related to data collection and generation \citep{manel_landscape_2003, storfer_putting_2007, manel_perspectives_2010, shafer_widespread_2013}. To our knowledge, this last point must contribute in particular to the fact that research on the environment and genetics of Cumacea is little explored. + +As stipulated in Darwin's hypothesis, individuals best adapted to their environment are likely to survive, reproduce and evolve in it \citep{darwin_origin_1859}. The objective of this study is to deepen and strengthen the natural selection hypothesis by examining whether there are one or more locations within Cumacea DNA sequences that could better correlate them with their environment. + + +\section{Materials and Methods}\label{materials-methods} + +\subsection{Description of the data} +The study area is located in a northern area of the North Atlantic, including the Icelandic Sea, the Denmark Strait, and the Norwegian Sea. The specimens included in this study were collected during the international IceAGE (Icelandic marine Animals: Genetic and Ecology; Cruise ship M85/3 in 2011; \citep{brix_iceage_2014, meisner_prefacebiodiversity_2018}) aboard the Meteor RV that explored the deep continental slopes and abyssal waters around Iceland \citep{meisner_prefacebiodiversity_2018}. The data considered in this study from the IceAGE expedition are available via the study of \cite{uhlir_adding_2021}. The sampling period for the specimens included in this study is from August 30 to September 22, 2011, and they were collected in a depth range of 316-2568 m. A description of the sampling plan and sample processing is provided in \cite{uhlir_adding_2021}. The steps of DNA extraction, PCR amplification and sequencing, as well as the extracted and aligned DNA sequences, are also available in the article by \cite{uhlir_adding_2021}. + +\subsection{Data pre-processing} +We considered data from the IceAGE project as well as data from the BOLD Systems database, both of which are available via the article by \cite{uhlir_adding_2021}. Given the large range of attributes from these databases, we made a succinct selection of the number of attributes and samples across them. Thus, we omitted attributes that were not relevant in the context of this study, that were completely or nearly invariable (non-numerical data) as well as those that had abundant missing data (> 95\%). We considered 62 of the 495 datasets from the IceAGE project. + +Subsequently, we calculated the variance for each of the selected numeric attributes in order to eliminate those with zero or low variance (cut-off ≥ 0.1): + +\begin{equation} +S^2 = \frac{\sum_{i=1}^{n} (x_i - \bar{x})^2}{n-1} +\end{equation} + +where \( S^2 \) is the variance of the sample, \( x_i \) represents each value in the data set, \( \bar{x} \) the average of all values in the data set, and \( n \) the number of values in the data set. + +Of the previously selected numerical attributes, only salinity was removed (\( S^2 = 0.02146629 \)). This selection of attributes and data resulted in a data table containing 62 rows (\( n=62 \)) and 18 columns (number of attributes). Figures \ref{fig:fig1a} and \ref{fig:fig1b} in the appendix were made from Python 3.11. + +\begin{figure}[] + \centering + \includegraphics[width=0.7\textwidth]{figure1.png} + \caption{Geographical coordinates at the beginning of the collection of each sample. \label{fig:fig1a}} +\end{figure} + +\begin{figure}[] + \centering + \includegraphics[width=0.7\textwidth]{figure2.png} + \caption{Geographical coordinates at the end of the collection of each sample. \label{fig:fig1b}} +\end{figure} + +From the IceAGE database, 14 attributes were selected. These consist of the geographical coordinates such as longitude (decimal) and latitude (decimal) taken at the beginning (see Figure \ref{fig:fig1a} and \ref{fig:fig1b}) and at the end of the collection of each sample. The increase in latitude, in particular, has been highlighted by several studies as being linked to the loss of marine biodiversity on a global scale \citep{rex_global-scale_1993, lambshead_latitudinal_2000, gage_diversity_2004}. These geographic data are divided into five sectors across the seas around Iceland: the Denmark Strait (\( n=28 \)), the Iceland Basin (\( n=15 \)), the Irminger Basin (\( n=12 \)), the Norwegian Sea (\( n=4 \)) and the Norwegian Basin (\( n=3 \)). For the environmental attributes in this database, we included the depth (m) at the beginning and end of sampling (see Figure \ref{fig:fig1c}) as well as the temperature (\( \degree C \)) (see Figure \ref{fig:fig1d}) and oxygen concentration (mg/L) (see Figure \ref{fig:fig1e}) of the water depending on the depth at which the specimens were sampled. These properties of water bodies are drivers of deep-sea biodiversity and biogeography with oxygen being a limiting factor for living organisms \citep{keeling_ocean_2010}. In addition to these contributions, the increase in depth \citep{rex_global_2006, roberts_cold-water_2009, costello_marine_2017} as well as the decrease in water temperature at depth \citep{lambshead_latitudinal_2000} are also factors in the loss of marine biodiversity on a global scale. Meteorological parameters such as speed (m/s) (see Figure \ref{fig:fig1f}) and wind direction at the beginning and end of sampling were also included in our data given the contribution of wind to the restructuring of the benthic ecosystem through water transport \citep{saeedi_environmental_2022, waga_recent_2020}. The wind direction at the start of sampling consists of six orientations: South-West (\( n=22 \)), South (\( n=15 \)), North-East (\( n=9 \)), South-South-East (\( n=9 \)), North-West (\( n=5 \)) and East (\( n=2 \)); while the one at the end of the sampling is made up of seven orientations: South (\( n=15 \)), South-West (\( n=15 \)), North-East (\( n=9 \)), West-South-West (\( n=7 \)), South-East (\( n=6 \)), North-North-West (\( n=5 \)), South-South-East (\( n=3 \)) and East (\( n=2 \)). In addition, we have included the sedimentary characteristics of the sampling sites as factors influencing the distribution of Cumacea \citep{uhlir_adding_2021} and which, for the purposes of this study, fall into six categories: mud (\( n=30 \)), sandy mud (\( n=15 \)), sand (\( n=9 \)), forams (\( n=3 \)), muddy sand (\( n=3 \)) and gravel (\( n=2 \)). + +\begin{figure}[] + \centering + \includegraphics[width=0.7\textwidth]{figure3.avif} + \caption{Depth at the beginning and end of sampling. \label{fig:fig1c}} +\end{figure} + +\begin{figure}[] + \centering + \includegraphics[width=0.7\textwidth]{figure4.png} + \caption{Temperature (\( \degree C \)) of the water at sampling depth. \label{fig:fig1d}} +\end{figure} + +\begin{figure}[] + \centering + \includegraphics[width=0.7\textwidth]{figure5.webp} + \caption{Oxygen concentration (mg/L) of the water at sampling depth. \label{fig:fig1e}} +\end{figure} + +\begin{figure}[] + \centering + \includegraphics[width=0.7\textwidth]{figure6.png} + \caption{Wind speed (m/s) at the beginning and end of sampling. \label{fig:fig1f}} +\end{figure} + +In the BOLD Systems database, taxonomic ranks such as family, genus, and species of the sampled Cumacea were included in our data. These are composed of seven families of Cumacea: Diastylidae (\( n=21 \)), Lampropidae (\( n=13 \)), Leuconidae (\( n=12 \)), Nannastacidae (\( n=7 \)), Bodotriidae (\( n=4 \)), Ceratocumatidae (\( n=3 \)) and Pseudocumatidae (\( n=2 \)). A total of 21 species of Cumacea are found in our sample (see Figure \ref{fig:fig2}). + +\begin{figure}[] + \centering + \includegraphics[width=0.7\textwidth]{figure7.webp} + \caption{Taxonomic distribution of sampled Cumacea species. \label{fig:fig2}} +\end{figure} + +The habitat and water mass of the sampling points are the only attributes that were taken directly via Table 1 of \cite{uhlir_adding_2021}. Thus, the definitions of water bodies described by \cite{hansen_north_2000}, \cite{brix_distribution_2010} and \cite{ostmann_marine_2014} were used as a reference for the GIN seas around Iceland: Arctic Polar Water (APW, \( n=15 \)), Iceland Sea Overflow Water (ISOW, \( n=15 \)), North Atlantic Water (NAW, \( n=9 \)), Arctic Polar Water/Norwegian Sea Arctic Intermediate Water (APW/NSAIW, \( n=7 \)), warm Norwegian Sea Deep Water (NSDWw, \( n=8 \)), Labrador Sea Water (LSW, \( n=3 \)), cold Norwegian Sea Deep Water (NSDWc, \( n=3 \)) and Norwegian Sea Arctic Intermediate Water (NSAIW, \( n=2 \)). In terms of habitat, we considered the three categories used in \cite{uhlir_adding_2021}: deep sea (\( n=38 \)), shelf (\( n=15 \)) and slope (\( n=9 \)). + +The aligned DNA sequence of the mitochondrial 16S rRNA gene region of each of the samples will also be included in our analyses. Thus, we consider 62 of the 306 aligned DNA sequences that were used for phylogenetic analyses of \cite{uhlir_adding_2021}. Since some of the specimens in our sample have their DNA sequence aligned duplicated, or even quadrupled with a difference of one to two nucleotides, we consider the longest aligned DNA sequence for each of the specimens. + +\subsection{aPhyloGeo software} + +For our analyses, we use the cross-platform Python software aPhyloGeo designed to analyze phylogenetic trees using climate parameters. Developed by Nadia Tahiri, Georges Marceau and David Beauchemin, the latter offers tools to study the correlations between the genetics of species and their habitats, thus allowing the understanding of the evolution of species under different environmental conditions. The software process takes place in three main steps. + + The first step is to collect Cumacea DNA sequences of sufficient quality for the requirements of our results \citep{koshkarov_phylogeography_2022}. A total of 62 Cumacea samples were selected to represent 62 sequences of the gene mitochondrial 16S rRNA. Subsequently, we included 6 climatic factors, namely the temperature and O2 concentration of the water as well as the wind speed and direction at the beginning and end of the sample. We also included 9 geographical factors, such as the body of water, the type of habitat and the type of sediment where the samples were collected. The latitude, longitude and depth of sample collection at the beginning and end of sampling were also considered among our geographical parameters. + + In the second step, the trees were generated with climatic, geographical and genetic data. For the geographic parameters, we calculated the dissimilarity between each pair of data from different geographic conditions, which produced a symmetric square matrix. From this matrix, the neighbor junction algorithm was used to design the climate tree. The same approach was applied to climatic and genetic data. Using the 62 sequences of the gene of mitochondrial 16S rRNA, phylogenetic reconstruction is repeated to build gene trees, considering only the data within a range that moves along the alignment. This displacement can vary depending on the steps and window size set by the user (their length is defined by the number of base pairs (pb)) \citep{koshkarov_phylogeography_2022}. + + In the third step, the phylogenetic trees built in each sliding window are compared to climatic and geographic parameters using the Robinson and Foulds (RF) topological distance \citep{robinson_comparison_1981, koshkarov_phylogeography_2022}. The distance was normalized by 2n-6, where n represents the number of taxa. The approach also considers bootstraping. Thus, the use of the sliding window ensures detailed identification of regions with high genetic mutation rates \citep{koshkarov_phylogeography_2022}. + +In short, we want to demonstrate a potential correlation between parts of the genes containing a high rate of mutations according to the geographical distribution of Cumacea samples. + +\section{Conclusion}\label{conclusion} + +The objective of this study is to perform an in-depth analysis of the influence of extreme climatic variables and environmental characteristics around Iceland on Cumacea (crustaceans: Peracarida) based on phylogeographic analysis. To date, we have selected relevant attributes for our study based on data from the IceAGE project, BOLD Systems, and the study by \cite{uhlir_adding_2021} and eliminated those that were not relevant to this study as well as those that had low variance (salinity, \( S^2 = 0.02146629 \)) or abundant missing data (>95\%). Thus, the first part consisted mainly of literature review, data collection, data pre-processing, and data analysis. + +For the upcoming fall semester, we are planning several crucial steps. First, we'll cluster our data to better understand climate data partitioning. Next, we'll update our Python package (in beta), dedicated to simplifying phylogeographic analyses. We also plan to conduct a thorough genetic analysis to examine the genetic diversity of our samples. In addition, we will analyze the cross-integration of climate and genetic data to better understand the interactions between the environment and the genetics of the populations studied. Finally, we plan to submit a scientific paper before the end of November. \ No newline at end of file diff --git a/papers/Gagnon_Keke_Tahiri_2024/mybib.bib b/papers/Gagnon_Keke_Tahiri_2024/mybib.bib new file mode 100644 index 0000000000..497c12f50e --- /dev/null +++ b/papers/Gagnon_Keke_Tahiri_2024/mybib.bib @@ -0,0 +1,1833 @@ +@article{brix_distributional_2018, + title = {Distributional patterns of isopods ({Crustacea}) in {Icelandic} and adjacent waters}, + volume = {48}, + issn = {1867-1616, 1867-1624}, + url = {http://link.springer.com/10.1007/s12526-018-0871-z}, + doi = {10.1007/s12526-018-0871-z}, + language = {en}, + number = {2}, + urldate = {2024-04-05}, + journal = {Marine Biodiversity}, + author = {Brix, Saskia and Stransky, Bente and Malyutina, Marina and Pabis, Krzysztof and Svavarsson, Jörundur and Riehl, Torben}, + month = jun, + year = {2018}, + pages = {783--811}, +} + +@article{ostmann_marine_2014, + title = {Marine {Environment} {Around} {Iceland}: {Hydrography}, {Sediments} and {First} {Predictive} {Models} of {Icelandic} {Deep}-sea {Sediment} {Characteristics}}, + volume = {35}, + shorttitle = {Marine {Environment} {Around} {Iceland}}, + doi = {10.2478/popore-2014-0021}, + abstract = {Sediment samples and hydrographic conditions were studied at 28 stations around Iceland. At these sites, Conductivity−Temperature−Depth (CTD) casts were conducted to collect hydrographic data and multicorer casts were conducted to collect data on sediment characteristics including grain size distribution, carbon and nitrogen concentration, and chloroplastic pigment concentration. A total of 14 environmental predictors were used to model sediment characteristics around Iceland on regional scale. Two approaches were used: Multivariate Adaptation Regression Splines (MARS) and randomForest regression models. RandomForest outperformed MARS in predicting grain size distribution. MARS models had a greater tendency to over− and underpredict sediment values in areas outside the environmental envelope defined by the training dataset. We provide first GIS layers on sediment characteristics around Iceland, that can be used as predictors in future models. Although models performed well, more samples, especially from the shelf areas, will be needed to improve the models in future.}, + journal = {Polish Polar Research}, + author = {Ostmann, Alexandra and Schnurr, Sarah and Martinez Arbizu, Pedro}, + month = jul, + year = {2014}, + pages = {151--176}, +} + +@article{hansen_north_2000, + title = {North {Atlantic}–{Nordic} {Seas} exchanges}, + volume = {45}, + issn = {0079-6611}, + url = {https://www.sciencedirect.com/science/article/pii/S007966119900052X}, + doi = {10.1016/S0079-6611(99)00052-X}, + abstract = {The northeastern part of the North Atlantic is unique in the sense that it is much warmer in the surface than other ocean areas at similar latitudes. The main reason for this is the large northward transport of heat that extends to high latitudes and crosses the Greenland–Scotland Ridge to enter the Nordic Seas and the Arctic. There the warm Atlantic water is converted to colder water masses that return southwards over the ridge partly as surface outflows and partly as overflows through the deep passages across the ridge. In this paper, the state of knowledge on the exchanges especially across the eastern part of the Greenland–Scotland Ridge is reviewed based on results from the ICES NANSEN (North Atlantic–Norwegian Sea Exchanges) project, from the Nordic WOCE project and from other sources. The accumulated evidence allows us to describe the exchanges in fair detail; the origins of the waters, the patterns of their flow towards and over the ridge and their ultimate fate. There is also increasing information on temporal variations of the exchanges although dynamical changes are still not well understood. Quantitative estimates for the volume transport of most of the overflow branches seem reasonably well established, and transport measurements of the Atlantic inflows to the Nordic Seas are approaching acceptable levels of confidence which allows preliminary budgets to be presented. The deep overflows are driven by pressure gradients set up by the formation of deep and intermediate water. The dominance of deep overflows over surface outflows in the water budget argues that this thermohaline forcing also dominates over direct wind stress and estuarine forcing in driving the Atlantic water inflow across the Greenland–Scotland Ridge, while wind stress seems to influence the characteristics and distribution of the Atlantic water north of the ridge.}, + number = {2}, + urldate = {2024-04-07}, + journal = {Progress in Oceanography}, + author = {Hansen, B and Østerhus, S}, + month = feb, + year = {2000}, + pages = {109--208}, +} + +@article{schnurr_composition_2014, + title = {Composition and distribution of selected munnopsid genera ({Crustacea}, {Isopoda}, {Asellota}) in {Icelandic} waters}, + volume = {84}, + issn = {0967-0637}, + url = {https://www.sciencedirect.com/science/article/pii/S0967063713002264}, + doi = {10.1016/j.dsr.2013.11.004}, + abstract = {The Greenland–Scotland Ridge (GSR) is a major topographic feature, extending from Greenland to Scotland. It constrains the water exchange between the northernmost North Atlantic Ocean and the Greenland, Iceland and Norwegian Seas (GIN Seas) and thus forms a potential barrier for faunal exchange from the Arctic to the North Atlantic (and vice versa). Recently an increase in Atlantic water inflow has been observed, leading to changes in physical parameters (i.e. temperature and salinity), which may have an impact on the resident fauna. In this study, we analyzed the composition and distribution of six selected genera of the isopod family Munnopsidae (Crustacea) occurring north and south of the GSR. We examined 82 epibenthic sledge samples and 26 additional sub-samples taken in the course of the Benthic Invertebrates of Icelandic Waters (BIOICE) and Icelandic Marine Animals: Genetics and Ecology (IceAGE) projects, respectively, covering a total depth range from 103 to 2752m depth. Overall, 58 of the evaluated stations originated in the area north of the GSR, while the remaining 50 samples were collected south of the ridge. In total, 10517 individuals could be assigned to 15 species, most belonging to the genus Eurycope Sars, 1864. Due to the presence of the GSR as well as differences in the environment, we expected significant dissimilarities in faunal composition between the two study areas. However, most species (8) occurred on both sides of the ridge, while four species were restricted to the region north of Iceland, and three to the region south of the ridge. Depth (or factors related to depth) appeared to be the most important factor in driving distributional patterns of the studied species. Temperature was also an important driver, but not to the same extent as depth. On the contrary, salinity and sediment type did not have much influence on munnopsid distribution patterns. Hence, the presence of the ridge does not restrict faunal exchange between the northern North Atlantic Ocean and GIN Seas for most of the investigated species, which may be explained by the good swimming abilities and the ecological flexibility of these munnopsid species.}, + urldate = {2024-04-07}, + journal = {Deep Sea Research Part I: Oceanographic Research Papers}, + author = {Schnurr, Sarah and Brandt, Angelika and Brix, Saskia and Fiorentino, Dario and Malyutina, Marina and Svavarsson, Jörundur}, + month = feb, + year = {2014}, + keywords = {BIOICE, distribution, Greenland–Scotland Ridge, IceAGE, Icelandic fauna, Isopoda, Munnopsidae}, + pages = {142--155}, +} + +@article{brix_iceage_2014, + title = {The {IceAGE} project – a follow up of {BIOICE}}, + volume = {35}, + issn = {0138-0338}, + url = {http://agro.icm.edu.pl/agro/element/bwmeta1.element.agro-9043a1bc-e6e5-41c1-8a18-1306cee46c6f}, + doi = {10.2478/popore-2014-0010}, + language = {EN}, + number = {2}, + urldate = {2024-04-07}, + journal = {Polish Polar Research}, + author = {Brix, S. and Meissner, K. and Stansky, B. and Halanych, K. M. and Jennings, R. M. and Kocot, K. M. and Svavarsson, J.}, + year = {2014}, + note = {Publisher: -}, +} + +@techreport{malmberg_hydrographic_2003, + type = {report}, + title = {Hydrographic conditions in {Icelandic} waters, 1990-1999}, + url = {https://ices-library.figshare.com/articles/report/Hydrographic_conditions_in_Icelandic_waters_1990-1999/19271738/1}, + abstract = {The main results of the hydrographic conditions in Icelandic waters in the 1990s reveal the same variability from year to year observed since the 1950s, including Atlantic, Polar, and Arctic periods in North Icelandic waters. Attention is paid to the hydro- graphic conditions in the warm water from the south (Inninger Current) which developed at the end of the 1990s into high saline conditions comparable with the period prior to the 1960s. This includes the northern component flowing into North Icelandic waters. The conditions in the East Icelandic Current also improved at the end of the 1990s with relatively high salinities. Thus the hydrobiological conditions in Icelandic waters were favourable at the end of the 1990s with regard to the various fish stocks. Article from Marine Science Symposia Vol. 219 - "Hydrobiological variability in the ICES Area, 1990-1999", symposium held in Edinburgh, 8-10 August 2001. To access the remaining articles please click on the keyword "MSS Vol. 219".}, + language = {en}, + urldate = {2024-04-07}, + institution = {ICES MSS Vol.219 - Hydrobiological variability in the ICES Area, 1990-1999}, + author = {Malmberg, Svend-Aage and Valdimarsson, Hedinn}, + month = sep, + year = {2003}, + doi = {10.17895/ices.pub.19271738.v1}, +} + +@article{brix_distribution_2010, + title = {Distribution and diversity of desmosomatid and nannoniscid isopods ({Crustacea}) on the {Greenland}–{Iceland}–{Faeroe} {Ridge}}, + volume = {33}, + issn = {1432-2056}, + url = {https://doi.org/10.1007/s00300-009-0729-8}, + doi = {10.1007/s00300-009-0729-8}, + abstract = {The distribution and diversity of isopods (Crustacea, Isopoda; families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916) was examined in Icelandic waters where a diversity of water masses (temperature range −0.9 to 12°C) occurs and the topography is characterized by the large and shallow Greenland–Iceland–Faeroe (GIF) Ridge extending across the North Atlantic in an east-west direction. Both families were species rich in the area, in total occurring with 34 species in 20 genera. Most of the species were restricted either to the north (10) or to the south (14) of the GIF Ridge, occurring either in cold (−0.8 to 2.8°C) or warm ({\textgreater}2°C) water masses. Five species were found on both sides of the Ridge, occurring at a wide range of temperatures (−0.9 to {\textgreater}4°C), while another five species extend across the GIF Ridge. Most species occurred in two and more water masses and the species north of the Ridge occurred usually within narrower temperature range than the species living south of the Ridge. The water masses in association with the Ridge seem to limit distribution of most species. Despite similar number of species occurring in the areas north and south of the Ridge, the areas differ considerably in diversity pattern with depth.}, + language = {en}, + number = {4}, + urldate = {2024-04-07}, + journal = {Polar Biology}, + author = {Brix, Saskia and Svavarsson, Jörundur}, + month = apr, + year = {2010}, + keywords = {BIOICE, Isopoda, Desmosomatidae, Greenland–Iceland–Faeroe Ridge, Iceland, Nannoniscidae, Water mass}, + pages = {515--530}, +} + +@article{meisner_benthic_2014, + title = {Benthic habitats around {Iceland} investigated during the {IceAGE} expeditions}, + volume = {35}, + issn = {0138-0338}, + url = {http://www.scopus.com/inward/record.url?scp=84905982926&partnerID=8YFLogxK}, + doi = {10.2478/popore-2014-0016}, + abstract = {During the IceAGE (Icelandic marine Animals - Genetics and Ecology) expeditions in waters around Iceland and the Faroe Islands in 2011 and 2013, visual assessments of habitats and the study of surface sediment characteristics were undertaken in 119-2750 m water depth. Visual inspection was realized by means of an epibenthic sled equipped with a digital underwater video camcorder and a still camera. For determination of surface sediment characteristics a subsample of sediment from box corer samples or different grabs was collected and analyzed in the lab. Muddy bottoms predominated in the deep basins (Iceland Basin, Irminger Basin, deep Norwegian and Iceland Seas), while sand and gravel dominated on the shelves and the ridges, and in areas with high currents. Organic contents were highest in the deep Norwegian and Iceland Seas and in the Iceland Basin, and at these sites dense aggregations of mobile epibenthic organisms were observed. Large dropstones were abundant in the Iceland Sea near the shelf and in the Denmark Strait. The dropstones carried diverse, sessile epibenthic fauna, which may be underestimated using traditional sampling gear. The paper supplies new background information for studies based on IceAGE material, especially studies related to ecology and taxonomy.}, + number = {2}, + urldate = {2024-04-07}, + journal = {Polish Polar Research}, + author = {Meißner, Karin and Brenke, Nils and Svavarsson, Jörundur}, + year = {2014}, + keywords = {Benthic habitat, Icelandic waters, North Atlantic, Sediment characteristics, Visual assessment}, + pages = {177--202}, +} + +@article{meisner_prefacebiodiversity_2018, + title = {Preface—biodiversity of {Icelandic} waters}, + volume = {48}, + issn = {1867-1624}, + url = {https://doi.org/10.1007/s12526-018-0884-7}, + doi = {10.1007/s12526-018-0884-7}, + language = {en}, + number = {2}, + urldate = {2024-04-07}, + journal = {Marine Biodiversity}, + author = {Meißner, Karin and Brix, Saskia and Halanych, Kenneth M. and Jażdżewska, Anna M.}, + month = jun, + year = {2018}, + pages = {715--718}, +} + +@article{lavin_evolution_1985, + title = {The evolution of freshwater diversity in the threespine stickleback ({Gasterosteus} aculeatus): site-specific differentiation of trophic morphology}, + volume = {63}, + issn = {0008-4301}, + shorttitle = {The evolution of freshwater diversity in the threespine stickleback ({Gasterosteus} aculeatus)}, + url = {https://cdnsciencepub.com/doi/abs/10.1139/z85-393}, + doi = {10.1139/z85-393}, + abstract = {To assess interpopulation levels of morphological variability populations of Gasterosteus aculeatus were sampled from lakes within the upper Cowichan River system (Vancouver Island, British Columbia). Phenotypic divergence between populations is assumed to be a postglacial event. Nine characters were scored; eight were related to feeding and the ninth character was lateral plate number. All populations were the low plate morph; however, populations of Gasterosteus in lakes lacking piscivorous fish had significantly fewer lateral plates than populations in lakes with predatory fish species. Two distinct trophic "morphotypes" were identified, each one associated with a specific lake environment. Populations inhabiting benthic-dominated environments were found to possess reduced gill raker number and reduced gill raker length but increased upper jaw length relative to populations from limnetic environments. We propose that the interpopulation variability in trophic morphology is a response to trophic resource differences between lakes.}, + number = {11}, + urldate = {2024-04-07}, + journal = {Canadian Journal of Zoology}, + author = {Lavin, P. A. and Mcphail, J. D.}, + month = nov, + year = {1985}, + note = {Publisher: NRC Research Press}, + pages = {2632--2638}, +} + +@article{jochumsen_bottom_2016, + title = {Bottom temperature and salinity distribution and its variability around {Iceland}}, + volume = {111}, + issn = {0967-0637}, + url = {https://www.sciencedirect.com/science/article/pii/S0967063715300509}, + doi = {10.1016/j.dsr.2016.02.009}, + abstract = {The barrier formed by the Greenland–Scotland-Ridge (GSR) shapes the oceanic conditions in the region around Iceland. Deep water cannot be exchanged across the ridge, and only limited water mass exchange in intermediate layers is possible through deep channels, where the flow is directed southwestward (the Nordic Overflows). As a result, the near-bottom water masses in the deep basins of the northern North Atlantic and the Nordic Seas hold major temperature differences. Here, we use near-bottom measurements of about 88,000 CTD (conductivity–temperature–depth) and bottle profiles, collected in the period 1900–2008, to investigate the distribution of near-bottom properties. Data are gridded into regular boxes of about 11km size and interpolated following isobaths. We derive average spatial temperature and salinity distributions in the region around Iceland, showing the influence of the GSR on the near-bottom hydrography. The spatial distribution of standard deviation is used to identify local variability, which is enhanced near water mass fronts. Finally, property changes within the period 1975–2008 are presented using time series analysis techniques for a collection of grid boxes with sufficient data resolution. Seasonal variability, as well as long term trends are discussed for different bottom depth classes, representing varying water masses. The seasonal cycle is most pronounced in temperature and decreases with depth (mean amplitudes of 2.2°C in the near surface layers vs. 0.2°C at depths {\textgreater}500m), while linear trends are evident in both temperature and salinity (maxima in shallow waters of +0.33°C/decade for temperature and +0.03/decade for salinity).}, + urldate = {2024-04-08}, + journal = {Deep Sea Research Part I: Oceanographic Research Papers}, + author = {Jochumsen, Kerstin and Schnurr, Sarah M. and Quadfasel, Detlef}, + month = may, + year = {2016}, + keywords = {Average hydrographic conditions near Iceland, Hydrographic variability, Seasonal cycle, Species distribution modelling}, + pages = {79--90}, +} + +@article{winton_effect_1997, + title = {The {Effect} of {Cold} {Climate} upon {North} {Atlantic} {Deep} {Water} {Formation} in a {Simple} {Ocean}–{Atmosphere} {Model}}, + volume = {10}, + issn = {0894-8755, 1520-0442}, + url = {https://journals.ametsoc.org/view/journals/clim/10/1/1520-0442_1997_010_0037_teoccu_2.0.co_2.xml}, + doi = {10.1175/1520-0442(1997)010<0037:TEOCCU>2.0.CO;2}, + abstract = {Abstract The sensitivity of North Atlantic Deep Water formation to variations in mean surface temperature is explored with a meridional-vertical plane ocean model coupled to an energy balance atmosphere. It is found that North Atlantic Deep Water formation is favored by a warm climate, while cold climates are more likely to produce Southern Ocean deep water or deep-decoupling oscillations (when the Southern sinking region is halocline covered). This behavior is traced to a cooling-induced convective instability near the North Atlantic sinking region, that is, to unstable horizontal spreading of a halocline that stratifies part of the region. Under the convective instability it is found that climate cooling is generally equivalent to increased freshwater forcing. This is because in a cold climate, high-latitude water masses approach the temperature of maximum density and the convection-driving, upward thermal buoyancy flux induced by surface cooling becomes insufficient to overcome the stratifying effect of surface freshening (a downward buoyancy flux). An extensive halocline is then formed and this halocline interferes with the heat loss necessary for the steady production of North Atlantic Deep Water.}, + language = {EN}, + number = {1}, + urldate = {2024-04-08}, + journal = {Journal of Climate}, + author = {Winton, Michael}, + month = jan, + year = {1997}, + note = {Publisher: American Meteorological Society +Section: Journal of Climate}, + pages = {37--51}, +} + +@article{ga_global_2007, + title = {Global climate projections}, + url = {https://cir.nii.ac.jp/crid/1573105974829939712}, + urldate = {2024-04-08}, + journal = {Climate change 2007 : the physical science basis. Contribution of working Group I to the fourth assessment report of the intergovernmental panel on climate change}, + author = {Ga, Meehl}, + year = {2007}, + note = {Publisher: Cambridge University Press}, + pages = {747--845}, +} + +@article{lohmann_sea_1998, + title = {Sea {Ice} {Effects} on the {Sensitivity} of the {Thermohaline} {Circulation}}, + volume = {11}, + issn = {0894-8755}, + url = {https://www.jstor.org/stable/26244230}, + abstract = {ABSTRACT The authors investigate the sensitivity of the thermohaline circulation (THC) with respect to a subpolar salinity perturbation. Such perturbation simulates a freshwater release caused by retreating glaciers or anomalous sea ice. The feedback mechanisms amplifying or damping the initial anomaly are analyzed in the coupled ocean–atmosphere–sea ice model. Their understanding is essential for modeling climate variability on decadal and longer timescales. A 3D ocean circulation model is coupled to an atmospheric energy balance and a thermodynamic sea ice model. The perturbation in the North Atlantic’s subpolar salinity causes a cessation of deep convection and a climate state with decreased oceanic heat transport, decreased high-latitude atmospheric temperature, and larger sea ice extent. The sea ice isolates the atmosphere from the warmer ocean, reducing the heat flux and thus the vertical mixing in the ocean. This change in the local buoyancy flux weakens the large-scale circulation. High-latitude cooling cannot compensate for the freshening since the ocean temperature cannot fall below the freezing point. Because deep convection is suppressed where sea ice is present, North Atlantic deep water formation is rather sensitive to the formation of sea ice. The insulating effect of sea ice is more important than its impact on salinity in our experiments. Different types of boundary conditions are used to isolate relevant feedback processes. The stability of the THC depends crucially on the atmospheric model component. Active atmospheric heat transport allows continued deep water formation because the sea ice margin is shifted poleward.}, + number = {11}, + urldate = {2024-04-08}, + journal = {Journal of Climate}, + author = {Lohmann, Gerrit and Gerdes, Rüdiger}, + year = {1998}, + note = {Publisher: American Meteorological Society}, + pages = {2789--2803}, +} + +@article{meehl_global_2007, + title = {Global climate projections. {Chapter} 10}, + url = {https://www.osti.gov/etdeweb/biblio/20962171}, + abstract = {The future climate change results assessed in this chapter are based on a hierarchy of models, ranging from Atmosphere-Ocean General Circulation Models (AOGCMs) and Earth System Models of Intermediate Complexity (EMICs) to Simple Climate Models (SCMs). These models are forced with concentrations of greenhouse gases and other constituents derived from various emissions scenarios ranging from non-mitigation scenarios to idealised long-term scenarios. In general, we assess non-mitigated projections of future climate change at scales from global to hundreds of kilometres. Further assessments of regional and local climate changes are provided in Chapter 11. Due to an unprecedented, joint effort by many modelling groups worldwide, climate change projections are now based on multi-model means, differences between models can be assessed quantitatively and in some instances, estimates of the probability of change of important climate system parameters complement expert judgement. New results corroborate those given in the Third Assessment Report (TAR). Continued greenhouse gas emissions at or above current rates will cause further warming and induce many changes in the global climate system during the 21st century that would very likely be larger than those observed during the 20th century.}, + language = {English}, + urldate = {2024-04-08}, + author = {Meehl, G. A. and Stocker, T. F. and Collins, W. D. and Friedlingstein, P. and Gaye, A. T. and Gregory, J. M. and Kitoh, A. and Knutti, R. and Murphy, J. M. and Noda, A. and Raper, S. C. B. and Watterson, I. G. and Weaver, A. J. and Zhao, Z. C.}, + month = sep, + year = {2007}, +} + +@article{meisner_prefacebiodiversity_2018-1, + title = {Preface—biodiversity of {Icelandic} waters}, + volume = {48}, + issn = {1867-1624}, + url = {https://doi.org/10.1007/s12526-018-0884-7}, + doi = {10.1007/s12526-018-0884-7}, + language = {en}, + number = {2}, + urldate = {2024-04-08}, + journal = {Marine Biodiversity}, + author = {Meißner, Karin and Brix, Saskia and Halanych, Kenneth M. and Jażdżewska, Anna M.}, + month = jun, + year = {2018}, + pages = {715--718}, +} + +@article{halfar_danger_2007, + title = {Danger of {Deep}-{Sea} {Mining}}, + volume = {316}, + url = {https://www.science.org/doi/full/10.1126/science.1138289}, + doi = {10.1126/science.1138289}, + number = {5827}, + urldate = {2024-04-08}, + journal = {Science}, + author = {Halfar, Jochen and Fujita, Rodney M.}, + month = may, + year = {2007}, + note = {Publisher: American Association for the Advancement of Science}, + pages = {987--987}, +} + +@article{mengerink_call_2014, + title = {A {Call} for {Deep}-{Ocean} {Stewardship}}, + volume = {344}, + url = {https://www.science.org/doi/full/10.1126/science.1251458}, + doi = {10.1126/science.1251458}, + number = {6185}, + urldate = {2024-04-08}, + journal = {Science}, + author = {Mengerink, Kathryn J. and Van Dover, Cindy L. and Ardron, Jeff and Baker, Maria and Escobar-Briones, Elva and Gjerde, Kristina and Koslow, J. Anthony and Ramirez-Llodra, Eva and Lara-Lopez, Ana and Squires, Dale and Sutton, Tracey and Sweetman, Andrew K. and Levin, Lisa A.}, + month = may, + year = {2014}, + note = {Publisher: American Association for the Advancement of Science}, + pages = {696--698}, +} + +@article{nath_environment_2000, + title = {Environment and {Deep}-{Sea} {Mining}: {A} {Perspective}}, + volume = {18}, + issn = {1064-119X}, + shorttitle = {Environment and {Deep}-{Sea} {Mining}}, + url = {https://doi.org/10.1080/10641190009353796}, + doi = {10.1080/10641190009353796}, + abstract = {As the quest for deep-sea mineral resources is gaining momentum, environment and ocean mining have become important aspects of study. Because many of these deposits occur in international waters, the concern for environmental conservation in view of the effects of deep-sea mining is resulting in these effects being studied in different oceans, and efforts to develop regulations governing this exploitation are also underway at national and international levels. The impact assessment of deep-sea mining needs to encompass a variety of subjects, including environmental, socioeconomic, technological, and legal aspects. At the same time, effects of in situ environmental conditions on mining activities also need to be considered for effecient performance by the mining system. Differences in the degree of impact have been noticed during the mining simulation experiments by different investigating agencies. Therefore, interparameter comparisons, standardization of methods, and improvement in mining design are important considerations for proper utilization of resources, conservation of environment, and cost efficiency of the mining operations.}, + number = {3}, + urldate = {2024-04-08}, + journal = {Marine Georesources \& Geotechnology}, + author = {Nath, B. Nagender and Sharma, R.}, + month = jul, + year = {2000}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/10641190009353796}, + keywords = {Deep-sea mining, environment, impact assessment, manganese nodules}, + pages = {285--294}, +} + +@article{wares_community_2002, + title = {Community genetics in the {Northwestern} {Atlantic} intertidal}, + volume = {11}, + issn = {1365-294X}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-294X.2002.01510.x}, + doi = {10.1046/j.1365-294X.2002.01510.x}, + abstract = {Our ability to make inferences about the processes acting upon a biological system can be dramatically improved through integration of information from other fields. In particular, this is true of the field of phylogeography, a discipline that attempts to describe geographical variation in species using neutral genetic diversity as a correlate of time. Through comparisons of information from multiple species, as well as background information about the abiotic environment and how it has changed over time, we should be able to reassemble many of the forces that were important in assembling the communities and community interactions found in a given region. Here I review the information available for coastal species in the northwestern Atlantic, and argue that an integration of ecological, genetic, geological and oceanographic information can illustrate emergent patterns of community genetics.}, + language = {en}, + number = {7}, + urldate = {2024-04-10}, + journal = {Molecular Ecology}, + author = {Wares, J. P.}, + year = {2002}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-294X.2002.01510.x}, + keywords = {community genetics, Monte Carlo, Northwest Atlantic, phylogeography}, + pages = {1131--1144}, +} + +@article{maggs_evaluating_2008, + title = {Evaluating {Signatures} of {Glacial} {Refugia} for {North} {Atlantic} {Benthic} {Marine} {Taxa}}, + volume = {89}, + copyright = {© 2008 by the Ecological Society of America}, + issn = {1939-9170}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1890/08-0257.1}, + doi = {10.1890/08-0257.1}, + abstract = {A goal of phylogeography is to relate patterns of genetic differentiation to potential historical geographic isolating events. Quaternary glaciations, particularly the one culminating in the Last Glacial Maximum ∼21 ka (thousands of years ago), greatly affected the distributions and population sizes of temperate marine species as their ranges retreated southward to escape ice sheets. Traditional genetic models of glacial refugia and routes of recolonization include these predictions: low genetic diversity in formerly glaciated areas, with a small number of alleles/haplotypes dominating disproportionately large areas, and high diversity including “private” alleles in glacial refugia. In the Northern Hemisphere, low diversity in the north and high diversity in the south are expected. This simple model does not account for the possibility of populations surviving in relatively small northern periglacial refugia. If these periglacial populations experienced extreme bottlenecks, they could have the low genetic diversity expected in recolonized areas with no refugia, but should have more endemic diversity (private alleles) than recently recolonized areas. This review examines evidence of putative glacial refugia for eight benthic marine taxa in the temperate North Atlantic. All data sets were reanalyzed to allow direct comparisons between geographic patterns of genetic diversity and distribution of particular clades and haplotypes including private alleles. We contend that for marine organisms the genetic signatures of northern periglacial and southern refugia can be distinguished from one another. There is evidence for several periglacial refugia in northern latitudes, giving credence to recent climatic reconstructions with less extensive glaciation.}, + language = {en}, + number = {sp11}, + urldate = {2024-04-10}, + journal = {Ecology}, + author = {Maggs, Christine A. and Castilho, Rita and Foltz, David and Henzler, Christy and Jolly, Marc Taimour and Kelly, John and Olsen, Jeanine and Perez, Kathryn E. and Stam, Wytze and Väinölä, Risto and Viard, Frédérique and Wares, John}, + year = {2008}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/08-0257.1}, + keywords = {climatic change, coalescence, genetic diversity, glaciations, haplotype networks, isolation, mitochondrial markers, recolonization, refugia}, + pages = {S108--S122}, +} + +@article{ilves_colonization_2010, + title = {Colonization and/or mitochondrial selective sweeps across the {North} {Atlantic} intertidal assemblage revealed by multi-taxa approximate {Bayesian} computation}, + volume = {19}, + copyright = {© 2010 Blackwell Publishing Ltd}, + issn = {1365-294X}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2010.04790.x}, + doi = {10.1111/j.1365-294X.2010.04790.x}, + abstract = {Intertidal and subtidal communities of the western and eastern coasts of the North Atlantic Ocean were greatly affected by Pleistocene glaciations, with some taxa persisting on both coasts, and others recolonizing after being extirpated on one coast during the Last Glacial Maximum. In the original spirit of comparative phylogeography, we conducted a comparative analysis using mtDNA sequence data and a hierarchical approximate Bayesian computation (ABC) approach for testing these two scenarios across 12 intertidal and subtidal coastal invertebrates spanning the North Atlantic to determine the temporal dynamics of species membership of these two ephemeral communities. Conditioning on a low gene-flow model, our results suggested that a colonization or mitochondrial selective sweep history was predominant across all taxa, with only the bivalve mollusc Mytilus edulis showing a history of trans-Atlantic persistence. Conditioning on a high gene-flow model weakened the support for this assemblage-level demographic history. The predominance of a colonization-type history also highlights concerns about analyses based on single-locus data where genetic hitchhiking may be incorrectly inferred as colonization. In conclusion, driving factors in shifting species range distributions and membership of ephemeral coastal communities could be species-specific environmental tolerances, species interactions, and/or stochastic demographic extinction. Through a re-examination of a long-standing question of North Atlantic phylogeography, we highlight the flexibility and statistical honesty of using a model-based ABC approach.}, + language = {en}, + number = {20}, + urldate = {2024-04-10}, + journal = {Molecular Ecology}, + author = {Ilves, Katriina L. and Huang, Wen and Wares, John P. and Hickerson, Michael J.}, + year = {2010}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2010.04790.x}, + keywords = {ABC, coalescent, comparative phylogeography, Last Glacial Maximum, statistical phylogeography}, + pages = {4505--4519}, +} + +@article{etter_phylogeography_2011, + title = {Phylogeography of a pan-{Atlantic} abyssal protobranch bivalve: implications for evolution in the {Deep} {Atlantic}}, + volume = {20}, + copyright = {© 2011 Blackwell Publishing Ltd}, + issn = {1365-294X}, + shorttitle = {Phylogeography of a pan-{Atlantic} abyssal protobranch bivalve}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2010.04978.x}, + doi = {10.1111/j.1365-294X.2010.04978.x}, + abstract = {The deep sea is a vast and essentially continuous environment with few obvious barriers to gene flow. How populations diverge and new species form in this remote ecosystem is poorly understood. Phylogeographical analyses have begun to provide some insight into evolutionary processes at bathyal depths ({\textless}3000 m), but much less is known about evolution in the more extensive abyssal regions ({\textgreater}3000 m). Here, we quantify geographical and bathymetric patterns of genetic variation (16S rRNA mitochondrial gene) in the protobranch bivalve Ledella ultima, which is one of the most abundant abyssal protobranchs in the Atlantic with a broad bathymetric and geographical distribution. We found virtually no genetic divergence within basins and only modest divergence among eight Atlantic basins. Levels of population divergence among basins were related to geographical distance and were greater in the South Atlantic than in the North Atlantic. Ocean-wide patterns of genetic variation indicate basin-wide divergence that exceeds what others have found for abyssal organisms, but considerably less than bathyal protobranchs across similar geographical scales. Populations on either side of the Mid-Atlantic Ridge in the North Atlantic differed, suggesting the Ridge might impede gene flow at abyssal depths. Our results indicate that abyssal populations might be quite large (cosmopolitan), exhibit only modest genetic structure and probably provide little potential for the formation of new species.}, + language = {en}, + number = {4}, + urldate = {2024-04-10}, + journal = {Molecular Ecology}, + author = {Etter, Ron J. and Boyle, Elizabeth E. and Glazier, Amanda and Jennings, Robert M. and Dutra, Ediane and Chase, Mike R.}, + year = {2011}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2010.04978.x}, + keywords = {phylogeography, ecological genetics, molecular evolution, Molluscs}, + pages = {829--843}, +} + +@article{aarbakke_discovery_2011, + title = {Discovery of {Pseudocalanus} moultoni ({Frost}, 1989) in {Northeast} {Atlantic} waters based on mitochondrial {COI} sequence variation}, + volume = {33}, + issn = {0142-7873}, + url = {https://doi.org/10.1093/plankt/fbr057}, + doi = {10.1093/plankt/fbr057}, + abstract = {The genus Pseudocalanus (Copepoda, Calanoida) consists of seven species, all of which are known to co-occur with two or more sibling species in some areas of their geographic ranges. Despite the ecological importance of this abundant genus, there is no available method that can reliably and accurately identify Pseudocalanus species without knowledge of origin. We present evidence of several observations of Pseudocalanus moultoni [Frost (1989) Can. J. Zool., 67, 525–551] in fjords of Svalbard and northern Norway; this species has previously been known to occur only on the east and west coasts of North America. Patterns of DNA sequence variation of the mitochondrial cytochrome oxidase subunit I (COI) gene allow us to confidently identify the species, discriminate it from co-occurring sibling species and infer relationships among the newly discovered and previously sampled P. moultoni populations. Our observations suggest that NE Atlantic populations of P. moultoni are self-sustaining and we discuss potential source populations and pathways of transport. In light of recent reports of climate-driven shifts in distributional ranges of marine zooplankton, accurate species identification is essential for monitoring and understanding marine ecosystems.}, + number = {10}, + urldate = {2024-04-10}, + journal = {Journal of Plankton Research}, + author = {Aarbakke, Ole Nicolai Staurland and Bucklin, Ann and Halsband, Claudia and Norrbin, Fredrika}, + month = oct, + year = {2011}, + pages = {1487--1495}, +} + +@article{rex_deep-sea_2011, + title = {Deep-{Sea} {Biodiversity}: {Pattern} and {Scale}}, + volume = {61}, + shorttitle = {Deep-{Sea} {Biodiversity}}, + doi = {10.1525/bio.2011.61.4.17}, + journal = {BioScience}, + author = {Rex, Michael and Etter, Ron}, + month = apr, + year = {2011}, + pages = {327--328}, +} + +@book{rex_deep-sea_2010, + title = {Deep-sea {Biodiversity}: {Pattern} and {Scale}}, + isbn = {978-0-674-03607-9}, + shorttitle = {Deep-sea {Biodiversity}}, + abstract = {Frigid, dark, and energy-deprived, the deep sea was long considered hostile to life. However, new sampling technologies and intense international research efforts in recent decades have revealed a remarkably rich fauna and an astonishing variety of novel habitats. These recent discoveries have changed the way we look at global biodiversity. In Deep-Sea Biodiversity, Michael Rex and Ron Etter present the first synthesis of patterns and causes of biodiversity in organisms that dwell in the vast sediment ecosystem that blankets the ocean floor. They provide the most comprehensive analysis to date of geographic variation in benthic animal abundance and biomass. The authors document geographic patterns of deep-sea species diversity and integrate potential ecological causes across scales of time and space. They also review the most recent molecular population genetic evidence to describe how and where evolutionary processes have generated the unique deep-sea fauna. Deep-Sea Biodiversity offers a new understanding of marine biodiversity that will be of general interest to ecologists and is crucial to responsible exploitation of natural resources at the deep-sea floor.}, + language = {en}, + publisher = {Harvard University Press}, + author = {Rex, Michael A. and Etter, Ron J.}, + year = {2010}, + note = {Google-Books-ID: 8d1gesF5QEEC}, + keywords = {Science / Earth Sciences / Oceanography, Science / Environmental Science, Science / Life Sciences / Biological Diversity, Science / Life Sciences / Biology, Science / Life Sciences / Marine Biology}, +} + +@article{wilson_historical_1998, + title = {Historical influences on deep-sea isopod diversity in the {Atlantic} {Ocean}}, + volume = {45}, + issn = {0967-0645}, + url = {https://www.sciencedirect.com/science/article/pii/S0967064597000465}, + doi = {10.1016/S0967-0645(97)00046-5}, + abstract = {Most isopod crustaceans in the North Atlantic deep sea belong to the suborder Asellota. In contrast, South Atlantic isopod faunas have a significant component of flabelliferan isopods, a phylogenetic clade that contains suborders derived evolutionarily later than the Asellota. The flabelliferans decrease diversity from shallow water to deep water and on a south-to-north latitudinal gradient. Although many asellote families are endemic to the deep sea, none of the flabelliferan families appear to have evolved in the abyss. Recent colonisations of the deep sea, which may have been limited to the southern hemisphere by oceanographic conditions, have significant consequences for observed regional diversities of some taxa. Instability in oceanographic conditions owing to glaciation and benthic storms may have further limited benthic species richness of the North Atlantic deep-sea benthos.}, + number = {1}, + urldate = {2024-04-10}, + journal = {Deep Sea Research Part II: Topical Studies in Oceanography}, + author = {Wilson, George D. F.}, + month = jan, + year = {1998}, + pages = {279--301}, +} + +@article{havermans_genetic_2013, + title = {Genetic and {Morphological} {Divergences} in the {Cosmopolitan} {Deep}-{Sea} {Amphipod} {Eurythenes} gryllus {Reveal} a {Diverse} {Abyss} and a {Bipolar} {Species}}, + volume = {8}, + issn = {1932-6203}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074218}, + doi = {10.1371/journal.pone.0074218}, + abstract = {Eurythenes gryllus is one of the most widespread amphipod species, occurring in every ocean with a depth range covering the bathyal, abyssal and hadal zones. Previous studies, however, indicated the existence of several genetically and morphologically divergent lineages, questioning the assumption of its cosmopolitan and eurybathic distribution. For the first time, its genetic diversity was explored at the global scale (Arctic, Atlantic, Pacific and Southern oceans) by analyzing nuclear (28S rDNA) and mitochondrial (COI, 16S rDNA) sequence data using various species delimitation methods in a phylogeographic context. Nine putative species-level clades were identified within E. gryllus. A clear distinction was observed between samples collected at bathyal versus abyssal depths, with a genetic break occurring around 3,000 m. Two bathyal and two abyssal lineages showed a widespread distribution, while five other abyssal lineages each seemed to be restricted to a single ocean basin. The observed higher diversity in the abyss compared to the bathyal zone stands in contrast to the depth-differentiation hypothesis. Our results indicate that, despite the more uniform environment of the abyss and its presumed lack of obvious isolating barriers, abyssal populations might be more likely to show population differentiation and undergo speciation events than previously assumed. Potential factors influencing species’ origins and distributions, such as hydrostatic pressure, are discussed. In addition, morphological findings coincided with the molecular clades. Of all specimens available for examination, those of the bipolar bathyal clade seemed the most similar to the ‘true’ E. gryllus. We present the first molecular evidence for a bipolar distribution in a macro-benthic deep-sea organism.}, + language = {en}, + number = {9}, + urldate = {2024-04-10}, + journal = {PLOS ONE}, + author = {Havermans, Charlotte and Sonet, Gontran and d’Acoz, Cédric d’Udekem and Nagy, Zoltán T. and Martin, Patrick and Brix, Saskia and Riehl, Torben and Agrawal, Shobhit and Held, Christoph}, + month = sep, + year = {2013}, + note = {Publisher: Public Library of Science}, + keywords = {Antarctica, Cryptic speciation, Deep sea, Haplotypes, Islands, Phylogenetic analysis, Phylogeography, Population genetics}, + pages = {e74218}, +} + +@article{jennings_phylogeographic_2014, + title = {Phylogeographic {Estimates} of {Colonization} of {The} {Deep} {Atlantic} by {The} {Protobranch} {Bivalve} {Nucula} {Atacellana}}, + issn = {0138-0338, 2081-8262}, + url = {https://bibliotekanauki.pl/articles/2051166}, + abstract = {Icelandic waters, Protobranchia, population genetics, species origin, North Atlantic demographics}, + language = {en}, + number = {2}, + urldate = {2024-04-10}, + journal = {Polish Polar Research}, + author = {Jennings, Robert M. and Etter, Ron J.}, + year = {2014}, + pages = {261--278}, +} + +@article{brandt_biodiversity_1997, + title = {Biodiversity of peracarid crustaceans({Malacostraca}) from the shelf downto the deep {Arctic} {Ocean}}, + volume = {6}, + issn = {1572-9710}, + url = {https://doi.org/10.1023/A:1018318604032}, + doi = {10.1023/A:1018318604032}, + abstract = {During three expeditions with the RVs Meteor and Polarstern more than sixty thousand peracarids were sampled from the deep Arctic Ocean (northern North Atlantic) by means of an epibenthic sledge. Sampling areas were the Kolbeinsey Ridge north of Iceland (800–1100 m), the Northeast Water Polynya, off Greenland (45–517m), and 75°N east of Greenland (197–2681m). Until now 288 species of Peracarida have been identified to species level. These 288 species comprise 152 genera and 59 families of Amphipoda, Cumacea, Isopoda, Mysidacea and Tanaidacea. Thirty-eight genera were very frequent and were sampled at each expedition (these were 22 species of Isopoda, seven species of Cumacea, three species of Amphipoda and Mysidacea, each, and two species of Tanaidacea). Sixty genera are eurybathic, occurring at least over a depth range of 1000m, some even from the shelf up to 2681m depth. Only 10 genera are stenobathic, occurring only in the deep sea. No significant decrease in species number with depth or latitude could be observed. The influencing factors probably causing different community structures are diverse, ranging from food availability over substrate or hydrographical qualities to interspecific competition.}, + language = {en}, + number = {11}, + urldate = {2024-04-10}, + journal = {Biodiversity \& Conservation}, + author = {Brandt, Angelika}, + month = nov, + year = {1997}, + keywords = {Arctic ocean, biodiversity, Crustacea, environmental factors, history of biodiversity research, Peracarida}, + pages = {1533--1556}, +} + +@article{conlan_distribution_2008, + series = {Sea ice and life in a river-influenced arctic shelf ecosystem}, + title = {Distribution patterns of {Canadian} {Beaufort} {Shelf} macrobenthos}, + volume = {74}, + issn = {0924-7963}, + url = {https://www.sciencedirect.com/science/article/pii/S0924796307002059}, + doi = {10.1016/j.jmarsys.2007.10.002}, + abstract = {Variation in macrofaunal composition in relation to sediment and water variables was analysed in nine regions of the western Canadian Arctic on the Beaufort Shelf and in Amundsen Gulf. We hypothesized that benthic community composition was distinctive (1) in a recurrent polynya in Amundsen Gulf and (2) in upwelling regions (Cape Bathurst and Mackenzie Canyon) and (3) changed in a linear gradient across the Beaufort Shelf. Analysis was based on 497 taxa {\textgreater}0.4 mm from 134 samples at 52 stations sampled over 2002–4 in 11–1000 m water depth. Abundance ranged from 490.7 m−2 in eastern Amundsen Gulf to 17,950 m−2 off Cape Bathurst. (1) Community composition in Amundsen Gulf was not significantly different from the Beaufort Shelf at similar depth, indicating a lack of benthic effect of the polynya in Amundsen Gulf. (2) The Mackenzie Canyon macrofauna, although abundant and diverse, were similarly indistinct from the shelf community at similar depth. However, there was a 10-fold increase in inshore abundance in the upwelling region of Cape Bathurst due to large numbers of the amphipod Ampelisca macrocephala and the polychaete Barantolla americana, species that were not abundant elsewhere. (3) In the inshore fast ice and flaw lead regions of the Beaufort Shelf, under the influence of ice scour, storm effects, coastal erosion and the Mackenzie River, the macrofauna were dominated by the bivalve Portlandia arctica and the polychaete Micronephthys minuta. Offshore, where these influences were less and upwelling of deep Atlantic water occurred, the polychaete Maldane sarsi dominated. Faunal distribution across the Beaufort Shelf correlated with depth, water and sediment changes but was not significantly linear.}, + number = {3}, + urldate = {2024-04-10}, + journal = {Journal of Marine Systems}, + author = {Conlan, Kathleen and Aitken, Alec and Hendrycks, Ed and McClelland, Christine and Melling, Humfrey}, + month = dec, + year = {2008}, + keywords = {Amundsen Gulf, Beaufort Shelf, Benthos, Canadian Arctic, Cape Bathurst, Community structure, Fast ice, Flaw lead, Polynya, Upwelling}, + pages = {864--886}, +} + +@article{stransky_diversity_2010, + title = {Diversity and species composition of peracarids ({Crustacea}: {Malacostraca}) on the {South} {Greenland} shelf: spatial and temporal variation}, + volume = {33}, + issn = {1432-2056}, + shorttitle = {Diversity and species composition of peracarids ({Crustacea}}, + url = {https://doi.org/10.1007/s00300-009-0691-5}, + doi = {10.1007/s00300-009-0691-5}, + abstract = {The interannual variability in peracarid (Crustacea: Malacostraca; Amphipoda, Isopoda, Cumacea, Tanaidacea) species composition and diversity on the South Greenland shelf was studied at four stations over a sampling period of 3 years (2001, 2002 and 2004), using a Rauschert sled at depths of about 160 m. The South Greenland peracarids were relatively stable over the 3 years with respect to evenness and diversity. Moderate changes in temperature and salinity had negligible effects on the species composition, while sediment structure was found to be the most important environmental variable shaping the peracarid fauna.}, + language = {en}, + number = {2}, + urldate = {2024-04-10}, + journal = {Polar Biology}, + author = {Stransky, Bente and Svavarsson, Jörundur}, + month = feb, + year = {2010}, + keywords = {Peracarida, Greenland, Shelf, Spatial and temporal variation, Species distribution}, + pages = {125--139}, +} + +@article{hansen_crustacea_1916, + title = {Crustacea {Malacostraca}, {III}. {V}. {The} order {Isopoda}}, + volume = {3}, + url = {https://biostor.org/reference/144536}, + abstract = {Published in The Danish Ingolf-Expedition, in 1916, in volume 3, issue 5, pages 1-262}, + number = {5}, + urldate = {2024-04-10}, + journal = {The Danish Ingolf-Expedition}, + author = {Hansen, H. J.}, + year = {1916}, + pages = {1--262}, +} + +@book{just_amphipoda_1980, + title = {Amphipoda ({Crustacea}) of the {Thule} {Area}, {Northwest} {Greenland}: {Faunistics} and {Taxonomy}}, + isbn = {978-87-635-1133-9}, + shorttitle = {Amphipoda ({Crustacea}) of the {Thule} {Area}, {Northwest} {Greenland}}, + language = {en}, + publisher = {Museum Tusculanum Press}, + author = {Just, Jean}, + year = {1980}, +} + +@article{l_updated_1983, + title = {An updated phyletic classification and palaeohistory of the {Amphipoda}}, + url = {https://cir.nii.ac.jp/crid/1571698600685503104}, + urldate = {2024-04-10}, + journal = {Crustacean Phylogeny}, + author = {L, Bousfield E.}, + year = {1983}, + note = {Publisher: Museum of Natural History}, + pages = {257--277}, +} + +@article{svavarsson_distribution_1990, + series = {Deep-{Sea} {Biology}}, + title = {Distribution and diversity patterns of asellote isopods ({Crustacea}) in the deep {Norwegian} and {Greenland} {Seas}}, + volume = {24}, + issn = {0079-6611}, + url = {https://www.sciencedirect.com/science/article/pii/0079661190900395}, + doi = {10.1016/0079-6611(90)90039-5}, + abstract = {Distribution and diversity patterns of asellote isopods (Crustacea) of the deep Norwegian and Greenland Seas are described. The asellotes show the same pattern of rapid faunal change across the upper continental slope as commonly described elsewhere. Here the rate of species replacement is maximum at depths of 800–1000m, but decreases towards greater depths. The distribution of the asellotes shows some correlations to the distribution of sediment types. Species diversity is maximum at 800m and decreases with depth. The species diversity pattern is related here to heterogeneity of the sediments and different species immigration rates into shallow and deep Arctic waters.}, + number = {1}, + urldate = {2024-04-10}, + journal = {Progress in Oceanography}, + author = {Svavarsson, Jörundur and Brattegard, Torleiv and Strömberg, Jarl-Ove}, + month = jan, + year = {1990}, + pages = {297--310}, +} + +@article{svavarsson_deep-sea_1993, + title = {The {Deep}-{Sea} {Asellote} ({Isopoda}, {Crustacea}) {Fauna} of the {Northern} {Seas}: {Species} {Composition}, {Distributional} {Patterns} and {Origin}}, + volume = {20}, + issn = {0305-0270}, + shorttitle = {The {Deep}-{Sea} {Asellote} ({Isopoda}, {Crustacea}) {Fauna} of the {Northern} {Seas}}, + url = {https://www.jstor.org/stable/2845725}, + doi = {10.2307/2845725}, + abstract = {The marine asellote (Isopoda, Crustacea) fauna of the Northern Seas, i.e. the Norwegian, Greenland, Iceland and North Polar Seas, contains 106 species. Most of them occur in shallow waters, but the number of species declines rapidly with increased depth. Half the species are endemic and those occurring also outside the Northern Seas are mainly found in the North Atlantic. The endemism of species is low ({\textless}50\%) at depths {\textless}750 m, but becomes high ({\textgreater}60\%) at depths {\textgreater}750 m. Only a single endemic asellote genus is recorded from the Northern Seas. The low diversity of the deep Arctic asellote isopods is explained partly by a short evolutionary time of the fauna within this environment, but in particular due to isolation of the Greenland-Iceland-Faeroe Ridge, which acts asa barrier against the immigration of species into the Northern Seas and thus shapes the species composition. The hydrographic condition above the ridge may also have restricted the migration of deep-sea species into the Northern Seas. Consequently, the Arctic deep-sea asellote fauna consists predominantly of species belonging to less pronounced deep-sea families (e.g. Desmosomatidae and Nannoniscidae) and genera, or shallow water genera occurring in proximity to the Northern waters, while the most pronounced deep-sea families and genera are poorly represented (e.g. families Haploniscidae and Ischnomesidae) or even absent (e.g. genus Storthyngura). The Arctic deep-sea asellote fauna is considered to have originated mainly from the North Atlantic Ocean.}, + number = {5}, + urldate = {2024-04-10}, + journal = {Journal of Biogeography}, + author = {Svavarsson, Jorundur and Stromberg, Jarl-Ove and Brattegard, Torleiv}, + year = {1993}, + note = {Publisher: Wiley}, + pages = {537--555}, +} + +@article{a_peracarid_1995, + title = {Peracarid fauna ({Crustacea}, {Malacostraca}) of the {Northeast} {Water} {Polynya} off {Greenland}: documenting close benthic-pelagic coupling in the {Westwind} {Trough}}, + volume = {121}, + issn = {0171-8630, 1616-1599}, + shorttitle = {Peracarid fauna ({Crustacea}, {Malacostraca}) of the {Northeast} {Water} {Polynya} off {Greenland}}, + url = {https://www.int-res.com/abstracts/meps/v121/p39-51/}, + doi = {10.3354/meps121039}, + abstract = {Composition, abundance, and diversity of peracarids (Crustacea) were investigated over a period of 3 mo in the Northeast Water Polynya (NEW), off Greenland. Samples were collected from May to July 1993 during expeditions ARK IX/2 and 3 using an epibenthic +sledge on RV 'Polarstern'. Within the macrobenthic community peracarids were an important component of the shelf fauna and occurred in high abundance in this area together with polychaetes, molluscs and brittle stars. A total of 38322 specimens were +sampled from 22 stations. Cumacea attained the highest total abundance and Amphipoda the highest diversity. Isopoda were of medium abundance, Mysidacea less abundant, and Tanaidacea least abundant. In total 229 species were found. Differences in +composition, abundance and diversity do not reflect bathymetric gradients, but mainly the availability of food (phytoplankton and especially ice algae) and, hence, the temporal and spatial opening of the polynya. Thus primary production and hydrographic +conditions (lateral advection due to the anticyclonic gyre around Belgica Bank) are the main biological and physical parameters influencing the peracarid crustacean community, documenting a close coupling between primary production and the benthic +community in the eastern Westwind Trough. The high abundance of Peracarida, which are also capable of burrowing in the upper sediment layers, indicates their importance for benthic carbon cycling.}, + language = {en}, + urldate = {2024-04-10}, + journal = {Marine Ecology Progress Series}, + author = {A, Brandt}, + month = may, + year = {1995}, + keywords = {Crustacea . Peracarida . Greenland . Northeast Water Polynya . Abundance . Diversity . Benthic-pelagic coupling}, + pages = {39--51}, +} + +@article{brandt_species_1996, + title = {The species composition of the {Peracarid} fauna ({Crustacea}, {Malacostraca}) of the {Northeast} {Water} {Polynya} ({Greenland})}, + volume = {44}, + copyright = {Copyright (c) 1996}, + issn = {2794-6819}, + url = {https://tidsskrift.dk/meddrgroenland_biosci/article/view/142582}, + doi = {10.7146/mogbiosci.v44.142582}, + abstract = {The species composition of Crustacea, Peracarida was investigated over a period of almost three months in the Northeast Water Polynya (NEW) off Greenland. Samples were collected in May - July 1993 during the Polarstern expedition ARK IX/2-3 using an epibenthic sledge. Within the macrobenthos on the shelf, peracarids were an important component, besides polychaetes, molluscs and brittle stars. At 22 stations in depths from 45-517 m, about 38 000 specimens were identified and have been listed. +In total, 229 species belonging to 51 families, and 121 genera were found. Seven species assemblages were characterized: the "deep assemblage", the "shallow assemblage", the "Westwind Trough assemblage", the "Norske Trough assemblage", the "common species assemblage", the "high-accumulation area assemblage", and the "ice-associate assemblage". Differences in abundance and composition do not primarily reflect bathymetric gradients, but more the availability of food (phytoplankton, more importantly ice algae incorporation into the sediment) and therefore the temporal and spatial opening of the polynya. It is suggested that primary production, hydrography, and ice conditions (lateral advection due to the \ anticyclonic gyre around Belgica Bank, and upwelling at a southern fast-ice extension) are the main factors influencing the peracarid crustacean community.}, + language = {en}, + urldate = {2024-04-10}, + journal = {Meddelelser om Grønland. Bioscience}, + author = {Brandt, Angelika and Vassilenko, Stella and Piepenburg, Dieter and Thurston, Michael}, + month = mar, + year = {1996}, + pages = {30 pp.--30 pp.}, +} + +@article{brandt_peracarid_2007, + title = {Peracarid composition, diversity and species richness in the area of the {Northeast} {Water} polynya, {East} {Greenland} ({Crustacea}, {Malacostraca})}, + volume = {31}, + issn = {1432-2056}, + url = {https://doi.org/10.1007/s00300-007-0327-6}, + doi = {10.1007/s00300-007-0327-6}, + abstract = {During the ARK XI-2 expedition with RV Polarstern in September/October 1995, a transect of epibenthic sledge (EBS) samples was taken in the area of the Northeast Water Polynya off the Greenland coast, from the shelf down into the deep sea. A total of 85,304 specimens of Peracarida were collected at seven stations. These individuals comprised 45 families, 103 genera and 180 species. With regard to abundance, Cumacea occurred with highest numbers, 31,269, followed by Isopoda, Amphipoda, Mysidacea and Tanaidacea. Species richness was highest in Amphipoda with 94 species, followed by Isopoda with 43 species, Cumacea with 20 species, Tanaidacea with 15 and Mysidacea with 8 species. Species richness was highest at the shallowest station 37-016 and lowest at the deepest station 37-021, whereas the opposite pattern was found for abundance. Diversity and eveness were highest at the southernmost station and lowest at the deepest station. Amphipoda occurred more frequently at the shallower stations, while Cumacea were very frequent at the deepest station. Numbers of species were lowest for Cumacea at the deepest station, while Amphipoda and Isopoda generally occurred with high species richness at all stations. On the basis of the species composition stations were compared.}, + language = {en}, + number = {1}, + urldate = {2024-04-10}, + journal = {Polar Biology}, + author = {Brandt, Angelika and Berge, Jørgen}, + month = dec, + year = {2007}, + keywords = {Deep sea, Crustacea, Peracarida, Diversity, Greenland Sea, Northeast Water Polynya, Species composition, Species richness}, + pages = {15--22}, +} + +@article{brandt_peracarid_1995, + title = {Peracarid fauna ({Crustacea}, {Malacostraca}) of the {Northeast} {Water} {Polynya} off {Greenland}:documenting close benthic-pelagic coupling in the {Westwind} {Trough}}, + volume = {121}, + issn = {0171-8630, 1616-1599}, + shorttitle = {Peracarid fauna ({Crustacea}, {Malacostraca}) of the {Northeast} {Water} {Polynya} off {Greenland}}, + url = {http://www.int-res.com/abstracts/meps/v121/p39-51/}, + doi = {10.3354/meps121039}, + abstract = {Composition, abundance, and diversity of peracarids (Crustacea) were investigated over a period of 3 mo in the Northeast Water Polynya (NEW), off Greenland. Samples were collected from May to July 1993 during expeditions ARK IX/2 and 3 using an epibenthic sledge on RV 'Polarstern' Within the macrobenthic community peracarids were an important component of the shelf fauna and occurred in high abundance in this area together with polychaetes, molluscs and brittle stars. A total of 38322 specimens were sampled from 22 stations. Cumacea attained the highest total abundance and Amphipoda the highest d{\textasciitilde}versityI.sopoda were of medium abundance, Mysidacea less abundant, and Tanaidacea least abundant. In total 229 species were found. Differences in composition, abundance and diversity do not reflect bathymetric gradients, but mainly the availability of food (phytoplankton and especially ice algae) and, hence, the temporal and spatial opening of the polynya. Thus primary production and hydrographic condit{\textasciitilde}ons(lateral advection due to the ant{\textasciitilde}cyclonicgyre around Belgica Bank) are the main biological and physical parameters influencing the peracarid crustacean community, documenting a close coupling between primary production and the benthic community in the eastern Westwind Trough. The high abundance of Peracarida, which are also capable of burrowing in the upper sediment layers, indicates their importance for benthic carbon cycling.}, + language = {en}, + urldate = {2024-04-10}, + journal = {Marine Ecology Progress Series}, + author = {Brandt, A}, + year = {1995}, + pages = {39--51}, + file = {Brandt - 1995 - Peracarid fauna (Crustacea, Malacostraca) of the N.pdf:C\:\\Users\\Justin\\Zotero\\storage\\C6IFXIET\\Brandt - 1995 - Peracarid fauna (Crustacea, Malacostraca) of the N.pdf:application/pdf}, +} + +@article{uhlir_adding_2021, + title = {Adding pieces to the puzzle: insights into diversity and distribution patterns of {Cumacea} ({Crustacea}: {Peracarida}) from the deep {North} {Atlantic} to the {Arctic} {Ocean}}, + volume = {9}, + issn = {2167-8359}, + shorttitle = {Adding pieces to the puzzle}, + url = {https://peerj.com/articles/12379}, + doi = {10.7717/peerj.12379}, + abstract = {The Nordic Seas have one of the highest water-mass diversities in the world, yet large knowledge gaps exist in biodiversity structure and biogeographical distribution patterns of the deep macrobenthic fauna. This study focuses on the marine bottom-dwelling peracarid crustacean taxon Cumacea from northern waters, using a combined approach of morphological and molecular techniques to present one of the first insights into genetic variability of this taxon. In total, 947 specimens were assigned to 77 morphologically differing species, representing all seven known families from the North Atlantic. A total of 131 specimens were studied genetically (16S rRNA) and divided into 53 putative species by species delimitation methods (GMYC and ABGD). In most cases, morphological and molecular-genetic delimitation was fully congruent, highlighting the overall success and high quality of both approaches. Differences were due to eight instances resulting in either ecologically driven morphological diversification of species or morphologically cryptic species, uncovering hidden diversity. An interspecific genetic distance of at least 8\% was observed with a clear barcoding gap for molecular delimitation of cumacean species. Combining these findings with data from public databases and specimens collected during different international expeditions revealed a change in the composition of taxa from a Northern Atlantic-boreal to an Arctic community. The Greenland-Iceland-Scotland-Ridge (GIS-Ridge) acts as a geographical barrier and/or predominate water masses correspond well with cumacean taxa dominance. A closer investigation on species level revealed occurrences across multiple ecoregions or patchy distributions within defined ecoregions.}, + language = {en}, + urldate = {2024-04-10}, + journal = {PeerJ}, + author = {Uhlir, Carolin and Schwentner, Martin and Meland, Kenneth and Kongsrud, Jon Anders and Glenner, Henrik and Brandt, Angelika and Thiel, Ralf and Svavarsson, Jörundur and Lörz, Anne-Nina and Brix, Saskia}, + month = nov, + year = {2021}, + note = {Publisher: PeerJ Inc.}, + pages = {e12379}, +} + +@article{norrevang_list_1994, + title = {List of {BIOFAR} stations}, + volume = {79}, + issn = {0036-4827}, + url = {https://doi.org/10.1080/00364827.1994.10413557}, + doi = {10.1080/00364827.1994.10413557}, + abstract = {THE BIOFAR PROGRAMME It is expected that a large number of scientific papers on marine benthic animals from Faroese waters will be published in SARSIA and elsewhere in the coming years. The authors of these articles will need to include or refer to lists of sampling stations for detailed information. A complete list, giving information on all deployments during the BIOFAR programme, published in an easily obtainable marine biological journal should be very useful to most of the authors and other scientists interested in benthic fauna of the Faroese area, and would reduce space and printing costs for editors.}, + number = {3}, + urldate = {2024-04-10}, + journal = {Sarsia}, + author = {Nørrevang, Arne and Brattegard, Torleiv and Josefson, Alf B. and Sneli, Jon-Arne and Tendal, Ole S.}, + month = dec, + year = {1994}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/00364827.1994.10413557}, + pages = {165--180}, +} + +@article{omarsdottir_biodiversity_2013, + title = {Biodiversity of benthic invertebrates and bioprospecting in {Icelandic} waters}, + volume = {12}, + issn = {1572-980X}, + url = {https://doi.org/10.1007/s11101-012-9243-7}, + doi = {10.1007/s11101-012-9243-7}, + abstract = {Iceland is an island in the North Atlantic Ocean, with an exclusive economic zone of 200 nautical miles that is largely unexplored with respect to chemical constituents of the marine biota. Iceland is a geothermally active area and hosts both hot and cold adapted organisms on land and in the ocean around it. In particular, the confluence of cold and warm water masses and geothermal activity creates a unique marine environment that has not been evaluated for the potential of marine natural product diversity. Marine organisms need to protect themselves from other organisms trying to overgrow, and some need to secure their place on the bottom of the ocean. Unexplored and unique areas such as the hydrothermal vent site at the sea floor in Eyjafjordur are of particular interest. In 1992 a collaborative research programme on collecting and identifying benthic invertebrates around Iceland (BIOICE) was established, with participation of Icelandic and foreign institutes, universities and taxonomists on benthic invertebrates from all over the world. Since the programme started almost 2,000 species have been identified and of those 41 species are new to science. Our recent bioprospecting project is directed towards the first systematic investigation of the marine natural product diversity of benthic invertebrates occurring in Icelandic waters, and their potential for drug-lead discovery in several key therapeutic areas.}, + language = {en}, + number = {3}, + urldate = {2024-04-10}, + journal = {Phytochemistry Reviews}, + author = {Omarsdottir, Sesselja and Einarsdottir, Eydis and Ögmundsdottir, Helga M. and Freysdottir, Jona and Olafsdottir, Elin Soffia and Molinski, Tadeusz F. and Svavarsson, Jörundur}, + month = sep, + year = {2013}, + keywords = {Icelandic waters, Benthic invertebrates, Bioprospecting, Hydrothermal vent sites, Marine biodiversity}, + pages = {517--529}, +} + +@misc{haskolabokasafn_timaritis_nodate, + type = {Service}, + title = {Tímarit.is}, + url = {https://timarit.is/page/931534}, + abstract = {Fróðskaparrit}, + language = {is}, + urldate = {2024-04-10}, + author = {Háskólabókasafn, Landsbókasafn Íslands-}, + note = {Publisher: Landsbókasafn Íslands - Háskólabókasafn}, +} + +@article{rothlisberg_epibenthic_1976, + title = {An epibenthic sampler used to study the ontogeny of vertical migration of pandalus dordani ({Decapoda} caridea)}, + url = {https://www.academia.edu/18058230/An_epibenthic_sampler_used_to_study_the_ontogeny_of_vertical_migration_of_pandalus_dordani_Decapoda_caridea_}, + abstract = {species of pandalid shrimps, undergo regular diel changes in their vertical distribution (Tegelberg and Smith 1957; Alverson et al. 1960; Pearcy 1970, 1972; Robinson in press). Little is known, however, about the vertical distribution and diel}, + urldate = {2024-04-12}, + author = {Rothlisberg, Peter}, + month = jan, + year = {1976}, +} + +@article{brattegard_replicability_1991, + title = {Replicability of an epibenthic sampler}, + volume = {71}, + issn = {1469-7769, 0025-3154}, + url = {https://www.cambridge.org/core/journals/journal-of-the-marine-biological-association-of-the-united-kingdom/article/abs/replicability-of-an-epibenthic-sampler/B0287261A4AD9F013BDB76FA0C258C3F}, + doi = {10.1017/S0025315400037462}, + abstract = {Hyperbenthos was sampled at six stations on the western slope of the Norwegian Trough. Four hauls, two day and two night replicates were taken at each station. The replicates were analyzed based on all sampled individuals of Mysidacea and Decapoda Natantia using Shannon diversity index, Spearman rank correlation, G-test, Bray-Curtis similarity index and Correspondence Analysis. The sampler provided samples of mysids and shrimps with an acceptable level of replicability based on number of individuals and diversity. In a cost-efficient context it is satisfactory to take only one sample at a station.}, + language = {en}, + number = {1}, + urldate = {2024-04-12}, + journal = {Journal of the Marine Biological Association of the United Kingdom}, + author = {Brattegard, T. and Fosså, J. H.}, + month = feb, + year = {1991}, + pages = {153--166}, +} + +@article{rothlisberg_epibenthic_1977, + title = {An epibenthic sampler used to study the ontogeny of vertical migration of {Pandalus} jordani ({Decapoda}, {Caridea})}, + volume = {74}, + abstract = {Reprinted from Fishery bulletin: Volume 74(4), pages 994-997. Master files scanned at 600 ppi (256 Grayscale) using Capture Perfect 3.0.82 on a Canon DR-9080C in TIF format. PDF derivative scanned at 300 ppi (256 B\&W, 256 Grayscale), using Capture Perfect 3.0.82, on a Canon DR-9080C. CVista PdfCompressor 4.0 was used for pdf compression and textual OCR.}, + journal = {Fish Bull}, + author = {Rothlisberg, Peter and Pearcy, William}, + month = jan, + year = {1977}, +} + +@article{rothlisberg_epibenthic_nodate, + title = {{AN} {EPIBENTHIC} {SAMPLER} {USED} {TO} {STUDY} {THE} {ONTOGENY} {OF} {VERTICAL} {MIGRATION} {OF} {PANDA} {LUS} {JORDANI} ({DECAPODA} {CARIDEA})}, + language = {en}, + author = {Rothlisberg, Peter and Pearcy, William G}, + file = {Rothlisberg et Pearcy - AN EPIBENTHIC SAMPLER USED TO STUDY THE ONTOGENY O.pdf:C\:\\Users\\Justin\\Zotero\\storage\\P9LYMYYX\\Rothlisberg et Pearcy - AN EPIBENTHIC SAMPLER USED TO STUDY THE ONTOGENY O.pdf:application/pdf}, +} + +@misc{noauthor_epibenthic_nodate, + title = {An epibenthic sampler used to study the ontogeny of vertical migration of {Pandalus} jordani ({Decapoda}, {Caridea}) {\textbar} {Scientific} {Publications} {Office}}, + url = {https://spo.nmfs.noaa.gov/content/epibenthic-sampler-used-study-ontogeny-vertical-migration-pandalus-jordani-decapoda-caridea}, + urldate = {2024-04-12}, +} + +@book{rothlisberg_epibenthic_1976-1, + title = {An {Epibenthic} {Sampler} {Used} to {Study} the {Ontogeny} of {Vertical} {Migration} of {Pandalus} {Jordani} ({Decapoda} {Caridea})}, + language = {en}, + publisher = {Oregon State Sea Grant College Program}, + author = {Rothlisberg, Peter C. and Pearcy, William G.}, + year = {1976}, + note = {Google-Books-ID: Drik0AEACAAJ}, +} + +@article{brix_distribution_2010-1, + title = {Distribution and diversity of desmosomatid and nannoniscid isopods ({Crustacea}) on the {Greenland}–{Iceland}–{Faeroe} {Ridge}}, + volume = {33}, + issn = {1432-2056}, + url = {https://doi.org/10.1007/s00300-009-0729-8}, + doi = {10.1007/s00300-009-0729-8}, + abstract = {The distribution and diversity of isopods (Crustacea, Isopoda; families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916) was examined in Icelandic waters where a diversity of water masses (temperature range −0.9 to 12°C) occurs and the topography is characterized by the large and shallow Greenland–Iceland–Faeroe (GIF) Ridge extending across the North Atlantic in an east-west direction. Both families were species rich in the area, in total occurring with 34 species in 20 genera. Most of the species were restricted either to the north (10) or to the south (14) of the GIF Ridge, occurring either in cold (−0.8 to 2.8°C) or warm ({\textgreater}2°C) water masses. Five species were found on both sides of the Ridge, occurring at a wide range of temperatures (−0.9 to {\textgreater}4°C), while another five species extend across the GIF Ridge. Most species occurred in two and more water masses and the species north of the Ridge occurred usually within narrower temperature range than the species living south of the Ridge. The water masses in association with the Ridge seem to limit distribution of most species. Despite similar number of species occurring in the areas north and south of the Ridge, the areas differ considerably in diversity pattern with depth.}, + language = {en}, + number = {4}, + urldate = {2024-04-12}, + journal = {Polar Biology}, + author = {Brix, Saskia and Svavarsson, Jörundur}, + month = apr, + year = {2010}, + keywords = {BIOICE, Isopoda, Desmosomatidae, Greenland–Iceland–Faeroe Ridge, Iceland, Nannoniscidae, Water mass}, + pages = {515--530}, +} + +@article{riehl_field_2014, + title = {Field and {Laboratory} {Methods} for {DNA} {Studies} on {Deep}-sea {Isopod} {Crustaceans}}, + volume = {35}, + doi = {10.2478/popore-2014-0018}, + abstract = {Field and laboratory protocols that originally led to the success of published studies have previously been only briefly laid out in the methods sections of scientific publications. For the sake of repeatability, we regard the details of the methodology that allowed broad-range DNA studies on deep-sea isopods too valuable to be neglected. Here, a comprehensive summary of protocols for the retrieval of the samples, fixation on board research vessels, PCR amplification and cycle sequencing of altogether six loci (three mitochondrial and three nuclear) is provided. These were adapted from previous protocols and developed especially for asellote Isopoda from deep-sea samples but have been successfully used in some other peracarids as well. In total, about 2300 specimens of isopods, 100 amphipods and 300 tanaids were sequenced mainly for COI and 16S and partly for the other markers. Although we did not set up an experimental design, we were able to analyze amplification and sequencing success of different methods on 16S and compare success rates for COI and 16S. The primer pair 16S SF/SR was generally reliable and led to better results than universal primers in all studied Janiroidea, except Munnopsidae and Dendrotionidae. The widely applied universal primers for the barcoding region of COI are problematic to use in deep-sea isopods with a success rate of 45–79\% varying with family. To improve this, we recommend the development of taxon-specific primers.}, + journal = {Polish Polar Research}, + author = {Riehl, Torben and Brenke, Nils and Brix, Saskia and Driskell, Amy and Kaiser, Stefanie and Brandt, Angelika}, + month = jan, + year = {2014}, +} + +@misc{watling_world_2024, + title = {World {Cumacea} {Database}. {Accessed} at https://www.marinespecies.org/cumacea on yyyy-mm-dd}, + copyright = {Creative Commons Attribution 4.0 International}, + shorttitle = {World {Cumacea} {Database}. {Accessed} at https}, + url = {https://www.marinespecies.org/imis.php?dasid=544&doiid=354}, + doi = {10.14284/354}, + abstract = {A world checklist of Cumacea, compiled by taxonomic experts and based on peer-reviewed literature.}, + language = {en}, + urldate = {2024-04-13}, + publisher = {[object Object]}, + author = {Watling, Les and Gerken, Sarah}, + collaborator = {Gerken, Sarah and Watling, Les and {Flanders Marine Institute (VLIZ), Belgium}}, + year = {2024}, + keywords = {Biology, Biology \> Ecology - biodiversity, Biology \> Invertebrates, Cumacea}, + annote = {Other +Cumaceans are small crustaceans, generally 1-10mm in size, which occur from tidal to abyssal depths in marine (and brackish) waters throughout the world. They are found in the first few cms of sand or sand/mud substrates; while they may be locally abundant, their distributions are patchy. Cumaceans feed on microorganisms and organic matter and are, in turn, consumed by bottom feeding organisms including a number of fishes. + +These malacostracans are distinguished by a combination of features including a large carapace which covers many thorasic somites, a narrow, long abdomen, a forked tail, and, in many families, a telson. The sexes are conspicuously dimorphic: females lack pleopods (with one exception, of course!) and have a large brood chamber. The carapace is ornamented in many lineages and appendages are generally highly modified. The morphology of cumaceans is sufficiently distinctive that members of the order are easy to recognize.}, +} + +@misc{noauthor_worms_nodate, + title = {{WoRMS} - {World} {Register} of {Marine} {Species}}, + url = {https://www.marinespecies.org/}, + urldate = {2024-04-13}, +} + +@misc{worms_editorial_board_world_2024, + title = {World {Register} of {Marine} {Species}. {Available} from https://www.marinespecies.org at {VLIZ}. {Accessed} yyyy-mm-dd.}, + copyright = {Creative Commons Attribution 4.0 International}, + shorttitle = {World {Register} of {Marine} {Species}. {Available} from https}, + url = {https://www.marinespecies.org/imis.php?dasid=1447&doiid=170}, + doi = {10.14284/170}, + abstract = {An authoritative and comprehensive list of names of marine organisms, including information on synonymy. WoRMS contains both global and regional species lists.}, + language = {en}, + urldate = {2024-04-13}, + publisher = {[object Object]}, + author = {{WoRMS Editorial Board}}, + collaborator = {{WoRMS Steering Committee (SC)} and {Flanders Marine Institute (VLIZ), Belgium}}, + year = {2024}, + keywords = {Biology, Biology \> Ecology - biodiversity, Animalia, Bacteria, Chromista, Fungi, Plantae, Protozoa, Viruses}, + annote = {Other +The aim of a World Register of Marine Species (WoRMS) is to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. + +The content of WoRMS is controlled by taxonomic experts, not by database managers. WoRMS has an editorial management system where each taxonomic group is represented by one or more experts who have the authority over the content, and are responsible for controlling the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility to join them. + +This register of marine species grew out of the European Register of Marine Species (ERMS), and its combination with several other species registers maintained at the Flanders Marine Institute (VLIZ). Rather than building separate registers for all projects, and to make sure taxonomy used in these different projects is consistent, VLIZ developed a consolidated database called ‘Aphia’. A list of marine species registers included in Aphia is available on the website. MarineSpecies.org is the web interface for this database. The WoRMS is an idea that is being developed, and will combine information from Aphia with other authoritative marine species lists which are maintained by others (e.g. AlgaeBase, FishBase, Hexacorallia, NeMys). + +Resources to build MarineSpecies.org and Aphia were provided mainly by the EU Network of Excellence ‘Marine Biodiversity and Ecosystem Functioning’ (MarBEF), and also by the EU funded Species 2000 Europe and ERMS projects. Currently, funding is received through the LifeWatch project, where WoRMS is part of the LifeWatch Taxonomic Backbone. + +Aphia contains valid species names, synonyms and vernacular names, and extra information such as literature and biogeographic data. Besides species names, Aphia also contains the higher classification in which each scientific name is linked to its parent taxon. The classification used is a ‘compromise’ between established systems and recent changes. Its aim is to aid data management, rather than suggest any taxonomic or phylogenetic opinion on species relationships. + +Keeping WoRMS up-to-date is a continuous process. New information is entered daily by the taxonomic editors and by the members of the Data Management Team. Often data also come in from contributions of large datasets, such as global or regional species lists. No database of this size is without errors and omissions. We can’t promise to make no errors, but we do promise to follow up and give feedback on any communications pointing out errors. Feedback is very welcome! + +Access to the data can be obtained either through the online interface or through requesting a download of the database.}, +} + +@article{van_noorden_how_2022, + title = {How language-generation {AIs} could transform science}, + volume = {605}, + copyright = {2022 Nature}, + url = {https://www.nature.com/articles/d41586-022-01191-3}, + doi = {10.1038/d41586-022-01191-3}, + abstract = {Shobita Parthasarathy warns that software designed to summarize, translate and write like humans might exacerbate distrust in science.}, + language = {en}, + number = {7908}, + urldate = {2024-04-14}, + journal = {Nature}, + author = {Van Noorden, Richard}, + month = apr, + year = {2022}, + note = {Bandiera\_abtest: a +Cg\_type: News Q\&a +Publisher: Nature Publishing Group +Subject\_term: Machine learning, Language, Peer review}, + keywords = {Language, Machine learning, Peer review}, + pages = {21--21}, +} + +@techreport{macke_expeditions_2018, + address = {Bremerhaven, Germany}, + title = {The {Expeditions} {PS106}/1 and 2 of the {Research} {Vessel} {POLARSTERN} to the {Arctic} {Ocean} in 2017}, + author = {Macke, Andreas and Flores, Hauke}, + year = {2018}, + doi = {10.2312/BzPM_0719_2018}, + note = {ISSN: 1866-3192 +Num Pages: 171}, + pages = {1--171}, +} + +@article{rex_global-scale_1993, + title = {Global-scale latitudinal patterns of species diversity in the deep-sea benthos}, + volume = {365}, + copyright = {1993 Springer Nature Limited}, + issn = {1476-4687}, + url = {https://www.nature.com/articles/365636a0}, + doi = {10.1038/365636a0}, + abstract = {LATITUDINAL gradients of species diversity are ubiquitous features of terrestrial and coastal marine biotas, and they have inspired the development of theoretical ecology1–3. Since the discovery of high species diversity in the deep-sea benthos4, much has been learned about local5,6and regional7–9patterns of diversity. Variation in diversity on larger scales remains poorly described. Latitudinal gradients of diversity were unexpected because it was assumed that the environmental gradients that cause large-scale patterns in surface environments could not affect communities living at great depths10. Here we report that deep-sea bivalves, gastropods and isopods show clear latitudinal diversity gradients in the North Atlantic, and strong interregional variation in the South Atlantic. Many seemingly incompatible mechanisms have been proposed to explain deep-sea species diversity11. The existence of regular global patterns suggests that these mechanisms operate at different spatial and temporal scales.}, + language = {en}, + number = {6447}, + urldate = {2024-04-22}, + journal = {Nature}, + author = {Rex, Michael A. and Stuart, Carol T. and Hessler, Robert R. and Allen, John A. and Sanders, Howard L. and Wilson, George D. F.}, + month = oct, + year = {1993}, + note = {Publisher: Nature Publishing Group}, + keywords = {Humanities and Social Sciences, multidisciplinary, Science}, + pages = {636--639}, +} + +@article{lambshead_latitudinal_2000, + title = {Latitudinal diversity gradients in the deep sea with special reference to {North} {Atlantic} nematodes}, + volume = {194}, + issn = {0171-8630, 1616-1599}, + url = {https://www.int-res.com/abstracts/meps/v194/p159-167/}, + doi = {10.3354/meps194159}, + abstract = {The discovery of global-scale latitudinal gradients of declining biodiversity from the tropics to the pole for bivalves, gastropods and isopods in the deep North Atlantic has created a high degree of interest and controversy. This is because +such gradients are commonly associated with solar energy-temperature gradients in terrestrial and shallow water systems and it is difficult to see how these processes might apply to a diversity gradient in the deep North Atlantic, where productivity +increases northwards but diversity declines. Here, we compare biodiversity patterns from marine nematodes, the most abundant deep-sea metazoan, from the deep North Atlantic with previous results and show that rarefaction is potentially unsuitable for +large-scale biogeographic pattern analysis. We obtain a different pattern from that previously obtained for mollusc and isopod data. Nematode diversity, as measured by species count, shows a positive gradient between 13 to 56°N, which is consistent with +the hypothesis that this pattern is related to the productivity gradient in the food-starved deep North Atlantic. The Norwegian Sea appears to be an area of low diversity for reasons connected to historical-geographical processes.}, + language = {en}, + urldate = {2024-04-22}, + journal = {Marine Ecology Progress Series}, + author = {Lambshead, P. J. D. and Tietjen, John and Ferrero, Timothy and Jensen+, Preben}, + month = mar, + year = {2000}, + keywords = {North Atlantic, Deep sea, Latitudinal gradients, Nematodes}, + pages = {159--167}, +} + +@article{gage_diversity_2004, + series = {{ANDEEP} ({Antarctic} benthic {DEEP}-sea) biodiversity: colonization history and recent community patterns: a tribute to {Howard} {L}. {Sanders}}, + title = {Diversity in deep-sea benthic macrofauna: the importance of local ecology, the larger scale, history and the {Antarctic}}, + volume = {51}, + issn = {0967-0645}, + shorttitle = {Diversity in deep-sea benthic macrofauna}, + url = {https://www.sciencedirect.com/science/article/pii/S0967064504001511}, + doi = {10.1016/j.dsr2.2004.07.013}, + abstract = {High diversity in macrobenthos in the deep sea still lacks satisfactory explanation, even if this richness may not be exceptional compared to that in coastal soft sediments. Explanations have assumed a highly ecologically interactive, saturated local community with co-existence controlled by either niche heterogeneity, or spatio-temporal heterogeneity embodying disturbance. All have failed to provide convincing support. Local/regional scale biodiversity relationships support the idea of local richness in macrobenthos being predominantly dependent on the larger, rather local scale. Local-scale ecological interactions seem unlikely to have overriding importance in co-existence of species in the deep sea, even for relatively abundant, ‘core’ species with wide distributions. Variety in observed larger-scale pattern and the strong inter-regional pattern, particularly in the poorly known southern hemisphere, seem to have a pluralistic causation. These include regional-scale barriers and extinctions (e.g., Arctic), and ongoing adaptive zone re-colonisation (e.g., Mediterranean), along with other historical constraints on speciation and migration of species caused by changes in ocean and ocean-basin geometry. At the global scale lack of knowledge of the Antarctic deep sea, for example, blocks coherent understanding of latitudinal species diversity gradients. We need to reconcile emerging understanding of large-scale historical variability in the deep-sea environment—with massive extinctions among microfossil indicators as recently as the Pliocene—to results from cladistic studies indicating ancient lineages, such as asellote isopods, that have evolved entirely within the deep sea. The degree to which the great age, diversity, and high degree of endemism in Antarctic shelf benthos might have enriched biodiversity in the adjacent deep seas basins remains unclear. Basin confluence with the Atlantic, Indian and Pacific Oceans may have encouraged northwards dispersion of species from and into the deep Antarctic basins so that any regional identity is superficial. Interpretation of the Antarctic deep sea as a diversity pump for global deep-sea biodiversity may simply reflect re-colonisation, via basin confluence, of northern hemisphere areas impoverished by the consequences of rapid environmental change during the Quaternary.}, + number = {14}, + urldate = {2024-04-22}, + journal = {Deep Sea Research Part II: Topical Studies in Oceanography}, + author = {Gage, John D.}, + month = jul, + year = {2004}, + pages = {1689--1708}, +} + +@article{rex_global_2006, + title = {Global bathymetric patterns of standing stock and body size in the deep-sea benthos}, + volume = {317}, + issn = {0171-8630, 1616-1599}, + url = {https://www.int-res.com/abstracts/meps/v317/p1-8/}, + doi = {10.3354/meps317001}, + abstract = {We present the first global-scale analysis of standing stock (abundance and biomass) for 4 major size classes of deep-sea biota: bacteria, metazoan meiofauna, macrofauna and megafauna. The community standing stock decreases with depth; this is a universal phenomenon that involves a complex transition in the relative importance of the different size groups. Bacterial abundance and biomass show no decline with depth. All 3 animal size groups experience significant exponential decreases in both abundance and biomass. The abundance of larger animals is significantly lower and decreases more rapidly than for smaller groups. The resulting drop in average body size with depth confirms Thiel’s size-structure hypothesis on very large spatial scales. In terms of their proportion of total community biomass, smaller size classes replace larger size classes. The upper continental slope is dominated by macrofaunal biomass, and the abyss by bacterial and meiofaunal biomass. The dramatic decrease in total community standing stock and the ascendancy of smaller organisms with depth has important implications for deep-sea biodiversity. The bathyal zone (200 to 4000 m) affords more ecological and evolutionary opportunity in the form of energy availability for larger organisms, and consequently supports higher macrofaunal and megafaunal species diversity than the abyss ({\textgreater}4000 m).}, + language = {en}, + urldate = {2024-04-22}, + journal = {Marine Ecology Progress Series}, + author = {Rex, Michael A. and Etter, Ron J. and Morris, Jeremy S. and Crouse, Jenifer and McClain, Craig R. and Johnson, Nicholas A. and Stuart, Carol T. and Deming, Jody W. and Thies, Rebecca and Avery, Renee}, + month = jul, + year = {2006}, + keywords = {Deep sea, Benthos, Abundance, Biodiversity, Biomass, Body size}, + pages = {1--8}, +} + +@book{roberts_cold-water_2009, + title = {Cold-water {Corals}: {The} {Biology} and {Geology} of {Deep}-sea {Coral} {Habitats}}, + isbn = {978-0-521-88485-3}, + shorttitle = {Cold-water {Corals}}, + abstract = {"There are more coral species in deep, cold-waters than in tropical coral reefs. This broad-ranging treatment is the first to synthesise current understanding of all types of cold-water coral, covering their ecology, biology, palaeontology and geology. Beginning with a history of research in the field, the authors describe the approaches needed to study corals in the deep sea. They consider coral habitats created by stony scleractinian as well as octocoral species. The importance of corals as long-lived geological structures and palaeoclimate archives is discussed, in addition to ways in which they can be conserved. Topic boxes explain unfamiliar concepts, and case studies summarise significant studies, coral habitats or particular conservation measures. Written for professionals and students of marine science, this text is enhanced by an extensive glossary, online resources, and a unique collection of colour photographs and illustrations of corals and the habitats they form."--Cambridge University Press website, viewed 4 August 2009.}, + language = {en}, + publisher = {Cambridge University Press}, + author = {Roberts, J. Murray}, + year = {2009}, + note = {Google-Books-ID: L6X6UW7ZszIC}, +} + +@article{costello_marine_2017, + title = {Marine {Biodiversity}, {Biogeography}, {Deep}-{Sea} {Gradients}, and {Conservation}}, + volume = {27}, + issn = {0960-9822}, + url = {https://www.sciencedirect.com/science/article/pii/S0960982217305055}, + doi = {10.1016/j.cub.2017.04.060}, + abstract = {The oceans appear ideal for biodiversity — they have unlimited water, a large area, are well connected, have less extreme temperatures than on land, and contain more phyla and classes than land and fresh waters. Yet only 16\% of all named species on Earth are marine. Species richness decreases with depth in the ocean, reflecting wider geographic ranges of deep sea than coastal species. Here, we assess how many marine species are named and estimated to exist, paying particular regard to whether discoveries of deep-sea organisms, microbes and parasites will change the proportion of terrestrial to marine species. We then review what factors have led to species diversification, and how this knowledge informs conservation priorities. The implications of this understanding for marine conservation are that the species most vulnerable to extinction will be large and endemic. Unfortunately, these species are also the most threatened by human impacts. Such threats now extend globally, and thus the only refuges for these species will be large, permanent, fully protected marine reserves.}, + number = {11}, + urldate = {2024-04-22}, + journal = {Current Biology}, + author = {Costello, Mark J. and Chaudhary, Chhaya}, + month = jun, + year = {2017}, + pages = {R511--R527}, +} + +@article{roberts_cold_2009, + title = {Cold {Water} {Corals}: {The} {Biology} and {Geology} of {Deep}-{Sea} {Coral} {Habitats}}, + issn = {9780521884853}, + shorttitle = {Cold {Water} {Corals}}, + doi = {10.1017/CBO9780511581588}, + abstract = {There are more coral species in deep, cold-waters than in tropical coral reefs. This broad-ranging treatment is the first to synthesise current understanding of all types of cold-water coral, covering their ecology, biology, palaeontology and geology. Beginning with a history of research in the field, the authors describe the approaches needed to study corals in the deep sea. They consider coral habitats created by stony scleractinian as well as octocoral species. The importance of corals as long-lived geological structures and palaeoclimate archives is discussed, in addition to ways in which they can be conserved. Topic boxes explain unfamiliar concepts, and case studies summarize significant studies, coral habitats or particular conservation measures. Written for professionals and students of marine science, this text is enhanced by an extensive glossary, online resources, and a unique collection of color photographs and illustrations of corals and the habitats they form. © J. Roberts, A. Wheeler, A. Freiwald and S. Cairns 2009 and Cambridge University Press, 2009.}, + journal = {Cold-Water Corals: The Biology and Geology of Deep-Sea Coral Habitats}, + author = {Roberts, J. and Wheeler, Andy and Freiwald, Andre and Cairns, Stephen}, + month = dec, + year = {2009}, + pages = {1--350}, +} + +@article{keeling_ocean_2010, + title = {Ocean {Deoxygenation} in a {Warming} {World}}, + volume = {2}, + issn = {1941-1405, 1941-0611}, + url = {https://www.annualreviews.org/content/journals/10.1146/annurev.marine.010908.163855}, + doi = {10.1146/annurev.marine.010908.163855}, + abstract = {Ocean warming and increased stratification of the upper ocean caused by global climate change will likely lead to declines in dissolved O2 in the ocean interior (ocean deoxygenation) with implications for ocean productivity, nutrient cycling, carbon cycling, and marine habitat. Ocean models predict declines of 1 to 7\% in the global ocean O2 inventory over the next century, with declines continuing for a thousand years or more into the future. An important consequence may be an expansion in the area and volume of so-called oxygen minimum zones, where O2 levels are too low to support many macrofauna and profound changes in biogeochemical cycling occur. Significant deoxygenation has occurred over the past 50 years in the North Pacific and tropical oceans, suggesting larger changes are looming. The potential for larger O2 declines in the future suggests the need for an improved observing system for tracking ocean O2 changes.}, + language = {fr}, + number = {Volume 2, 2010}, + urldate = {2024-04-22}, + journal = {Annual Review of Marine Science}, + author = {Keeling, Ralph F. and Körtzinger, Arne and Gruber, Nicolas}, + month = jan, + year = {2010}, + note = {Publisher: Annual Reviews}, + pages = {199--229}, +} + +@misc{lead_artificial_2023, + title = {Artificial intelligence in scientific research: {Common} problems and potential solutions}, + shorttitle = {Artificial intelligence in scientific research}, + url = {https://sciencepolicy.ca/posts/artificial-intelligence-in-scientific-research-common-problems-and-potential-solutions/}, + abstract = {The recent emergence of large language model (LLM)-based chatbots like Open AI’s ChatGPT have ignited the public’s interest in artificial intelligence (AI). For the average AI enthusiast, LLM-based chatbots are a convenient tool that can be easily used to complete simple tasks such as writing mundane emails, explaining}, + language = {en-CA}, + urldate = {2024-04-24}, + journal = {CSPC}, + author = {Lead, Editorial}, + month = sep, + year = {2023}, +} + +@article{powers_open_2019, + title = {Open science, reproducibility, and transparency in ecology}, + volume = {29}, + copyright = {© 2018 The Authors Ecological Applications published by Wiley Periodicals, Inc. on behalf of Ecological Society of America}, + issn = {1939-5582}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eap.1822}, + doi = {10.1002/eap.1822}, + abstract = {Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility and also transparency. Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility can still be achieved. Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study. When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy. Expectations for computational reproducibility and transparency are shifting rapidly in the sciences. In this work, we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.}, + language = {en}, + number = {1}, + urldate = {2024-04-24}, + journal = {Ecological Applications}, + author = {Powers, Stephen M. and Hampton, Stephanie E.}, + year = {2019}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/eap.1822}, + keywords = {collaborative tools, data policy, data science, ecoinformatics, ecosystem, environmental science, open science, repeatability, replicability, reproducible, transparent, workflows}, + pages = {e01822}, +} + +@article{castelvecchi_are_2022, + title = {Are {ChatGPT} and {AlphaCode} going to replace programmers?}, + copyright = {2022 Springer Nature Limited}, + url = {https://www.nature.com/articles/d41586-022-04383-z}, + doi = {10.1038/d41586-022-04383-z}, + abstract = {OpenAI and DeepMind systems can now produce meaningful lines of code, but software engineers shouldn’t switch careers quite yet.}, + language = {en}, + urldate = {2024-04-24}, + journal = {Nature}, + author = {Castelvecchi, Davide}, + month = dec, + year = {2022}, + note = {Bandiera\_abtest: a +Cg\_type: News +Publisher: Nature Publishing Group +Subject\_term: Machine learning, Mathematics and computing}, + keywords = {Machine learning, Mathematics and computing}, +} + +@article{roberts_cold_2009-1, + title = {Cold {Water} {Corals}: {The} {Biology} and {Geology} of {Deep}-{Sea} {Coral} {Habitats}}, + issn = {9780521884853}, + shorttitle = {Cold {Water} {Corals}}, + doi = {10.1017/CBO9780511581588}, + abstract = {There are more coral species in deep, cold-waters than in tropical coral reefs. This broad-ranging treatment is the first to synthesise current understanding of all types of cold-water coral, covering their ecology, biology, palaeontology and geology. Beginning with a history of research in the field, the authors describe the approaches needed to study corals in the deep sea. They consider coral habitats created by stony scleractinian as well as octocoral species. The importance of corals as long-lived geological structures and palaeoclimate archives is discussed, in addition to ways in which they can be conserved. Topic boxes explain unfamiliar concepts, and case studies summarize significant studies, coral habitats or particular conservation measures. Written for professionals and students of marine science, this text is enhanced by an extensive glossary, online resources, and a unique collection of color photographs and illustrations of corals and the habitats they form. © J. Roberts, A. Wheeler, A. Freiwald and S. Cairns 2009 and Cambridge University Press, 2009.}, + journal = {Cold-Water Corals: The Biology and Geology of Deep-Sea Coral Habitats}, + author = {Roberts, J. and Wheeler, Andy and Freiwald, Andre and Cairns, Stephen}, + month = dec, + year = {2009}, + pages = {1--350}, +} + +@article{meisner_prefacebiodiversity_2018-2, + title = {Preface—biodiversity of {Icelandic} waters}, + volume = {48}, + doi = {10.1007/s12526-018-0884-7}, + journal = {Marine Biodiversity}, + author = {Meißner, Karin and Brix, Saskia and Halanych, Ken and Jazdzewska, Anna}, + month = apr, + year = {2018}, +} + +@article{brix_iceage_2014-1, + title = {The {IceAGE} project – a follow up of {BIOICE}}, + volume = {35}, + issn = {0138-0338}, + url = {http://agro.icm.edu.pl/agro/element/bwmeta1.element.agro-9043a1bc-e6e5-41c1-8a18-1306cee46c6f}, + doi = {10.2478/popore-2014-0010}, + language = {EN}, + number = {2}, + urldate = {2024-04-25}, + journal = {Polish Polar Research}, + author = {Brix, S. and Meissner, K. and Stansky, B. and Halanych, K. M. and Jennings, R. M. and Kocot, K. M. and Svavarsson, J.}, + year = {2014}, + note = {Publisher: -}, +} + +@article{saeedi_environmental_2022, + title = {The {Environmental} {Drivers} of {Benthic} {Fauna} {Diversity} and {Community} {Composition}}, + volume = {9}, + issn = {2296-7745}, + url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.804019}, + doi = {10.3389/fmars.2022.804019}, + abstract = {Establishing management programs to preserve the benthic communities along the NW Pacific and the Arctic Ocean (AO) requires a great understanding of the composition of communities and their responses to environmental stressors. In this study, we thus examine patterns of benthic community composition and patterns of species richness along the NW Pacific and Arctic Seas and investigate the most important environmental drivers of those patterns. Overall we find a trend of decreasing species richness towards higher latitudes and deeper waters, peaking in coastal waters of the eastern Philippines. The most dominant taxa along the entire study area were Arthropoda, Mollusca, Cnidaria, Echinodermata, and Annelida. We found that depth, not temperature, is the main driver of community composition along the NW Pacific and neighboring Arctic Seas. Depth has been previously suggested as a factor driving speciation in benthic fauna. Following depth, the most influential environmental drivers of community composition along the NW Pacific and the Arctic Ocean were silicate, light, and currents. For example, silicate in Hexactinellida, Holothuroidea, and Ophiuroidea; and light in Cephalopoda and Gymnolaemata had the highest correlation with community composition. In this study, based on a combination of new samples and open-access data, we show that different benthic communities might respond differently to future climatic changes based on their taxon-specific biological, physiological, and ecological characteristics. International conservation efforts and habitat preservation should take an adaptive approach and apply measures that take the differences between benthic communities in responding to future climate change into account. This facilitates implementing appropriate conservation management strategies and sustainable utilization of the NW Pacific and Arctic marine ecosystems.}, + language = {English}, + urldate = {2024-04-25}, + journal = {Frontiers in Marine Science}, + author = {Saeedi, Hanieh and Warren, Dan and Brandt, Angelika}, + month = mar, + year = {2022}, + note = {Publisher: Frontiers}, + keywords = {Arctic Ocean, Benthic fauna, community composition, deep sea, depth, NW Pacific, Shallow water, Silicate}, +} + +@article{waga_recent_2020, + title = {Recent change in benthic macrofaunal community composition in relation to physical forcing in the {Pacific} {Arctic}}, + volume = {43}, + issn = {1432-2056}, + url = {https://doi.org/10.1007/s00300-020-02632-3}, + doi = {10.1007/s00300-020-02632-3}, + abstract = {There is growing evidence that increased Pacific water transport into the Arctic affects the marine ecosystem. One of the theoretical predictions for a future Arctic characterized by such environmental change is that subarctic taxa will expand northward and invade the native Arctic ecosystem. This study focuses on variation in macrofaunal community composition and the influence of changing physical drivers at known benthic hotspots in the Pacific Arctic. The average number of macrofaunal family-level taxa has increased significantly south of St. Lawrence Island and in the Chirikov Basin, whereas the number of macrofaunal taxa in the southeastern Chukchi Sea showed no significant trend over the 2000–2013 time period. However, the Shannon–Weaver diversity index, based on abundance, did not mirror these regional changes in the number of macrofaunal taxa, indicating that the abundance of newly present taxa was negligible compared to the entire abundance already present. We also investigated temporal variations in meridional sea level gradient and local winds, which contribute 2/3 and 1/3 of the variation in northward volume transport at Bering Strait, respectively. There were significant increasing trends in the meridional sea level gradient and local winds, suggesting the increased northward seawater volume transports over the benthic hotspots could contribute to the expansion of subarctic taxa into these northern Arctic regions. Our data suggest an increase in macrofaunal taxa type with increasing current transport northward into the Pacific Arctic region that could have a strong influence in restructuring the benthic ecosystem in this region in the future.}, + language = {en}, + number = {4}, + urldate = {2024-04-25}, + journal = {Polar Biology}, + author = {Waga, Hisatomo and Hirawake, Toru and Grebmeier, Jacqueline M.}, + month = apr, + year = {2020}, + keywords = {Benthos, Diversity, Macrofauna composition, Pacific arctic, Volume transports}, + pages = {285--294}, +} + +@inproceedings{johannessen_relationship_1994, + address = {Berlin, Heidelberg}, + title = {The {Relationship} between {Surface} {Water} {Masses}, {Oceanographic} {Fronts} and {Paleoclimatic} {Proxies} in {Surface} {Sediments} of the {Greenland}, {Iceland}, {Norwegian} {Seas}}, + isbn = {978-3-642-78737-9}, + doi = {10.1007/978-3-642-78737-9_4}, + abstract = {A detailed study of paleoclimatic proxy data (stable isotopes, planktonic foraminiferal census data, carbonate content, and Ice Rafted Detritus (IRD)) in the surface sediments of the Greenland, Iceland and Norwegian Seas (GIN-seas) shows that different proxies are closely related to the surface water masses, to the position of oceanic fronts and to the sea ice extent. Both stable isotopes, foraminifers and sedimentological data differentiate between Polar water with extensive sea ice cover, Arctic water with only seasonal sea ice cover, and warm Atlantic water. The fronts that border these surface water masses are also well defined. Polar water is characterized by lower carbon and oxygen isotope values than Arctic water, and a slightly lower content of Neogloboquadrina pachyderma sinistral in the Polar Front region. Carbonate content is low and IRD input is high in Polar waters. Arctic water has highest carbon and oxygen isotope values, and is completely dominated by N. pachyderma sin. The Arctic Front is reflected by a clear isotopic gradient and by a strong switch from N. pachyderma sin. dominance to Globigerina quinqueloba dominance. Atlantic Water is defined by lower carbon and oxygen isotope values and by dominance of N. pachyderma dextral and increased amounts of Globigerina bulloides. The results have implications for paleoceanographic reconstructions of cold environments and point to the possibility of better defining sea ice margins and convective regions as well as frontal positions in past high latitude oceans. Applying these results to the Last Glacial Maximum and the Younger Dryas indicates more dynamic and less sea ice covered surface conditions in the GIN-seas than in earlier reconstructions.}, + language = {en}, + booktitle = {Carbon {Cycling} in the {Glacial} {Ocean}: {Constraints} on the {Ocean}’s {Role} in {Global} {Change}}, + publisher = {Springer}, + author = {Johannessen, Truls and Jansen, Eystein and Flatøy, Astrid and Ravelo, Ana Christina}, + editor = {Zahn, Rainer and Pedersen, Thomas F. and Kaminski, Michael A. and Labeyrie, Laurent}, + year = {1994}, + pages = {61--85}, +} + +@article{forsman_untersuchungen_nodate, + title = {Untersuchungen über die {Cumaceen} des {Skageraks}}, + url = {https://cir.nii.ac.jp/crid/1130282269090034944}, + language = {de}, + urldate = {2024-04-26}, + journal = {(No Title)}, + author = {Forsman, Bror}, +} + +@misc{noauthor_enequist_nodate, + title = {Enequist: {Studies} on the {Soft}-bottom {Amphipods} of... - {Google} {Scholar}}, + url = {https://scholar.google.com/scholar_lookup?&title=Studies%20of%20the%20soft-bottom%20amphipods%20of%20the%20Skagerak&journal=Zool%20Bidr%20Upps&volume=28&pages=1-491&publication_year=1949&author=Enequist%2CP}, + urldate = {2024-04-26}, +} + +@article{hessler_behavior_1989, + title = {Behavior of janiroidean isopods ({Asellota}), with special reference to deep-sea genera}, + volume = {74}, + issn = {0036-4827}, + url = {https://doi.org/10.1080/00364827.1989.10413424}, + doi = {10.1080/00364827.1989.10413424}, + abstract = {Knowledge about the behavior of deep-sea isopods is sparse, in spite of their importance (as judged from faunal diversity and numerical abundance) in deep-sea communities. Yet an understanding of the ecology of those communities ultimately requires information on where and how component species live. Many deep-sea isopod families and genera have shallow-water representatives at northern and southern high latitudes. Basic behavioral features of these taxa have been revealed through study of these shallow-waters forms. This report describes behavior seen in aquaria of species within the Janiridae, Munnidae, Paramunnidae, Ischnomesidae, Desmosomatidae, Eurycopidae, and Ilyarachnidae. Observations cover locomotion (walking, swimming, burrowing), feeding, grooming, respiration, brooding, and interindividual behavior. Several activities, particularly concerning grooming and respiration, characterize many of the taxa. Locomotory habits are strongly correlated with morphology, but borrowing is more common than has been predicted from body design, and taxa with natatory conformation were surprisingly reluctant to swim.}, + number = {3}, + urldate = {2024-04-26}, + journal = {Sarsia}, + author = {Hessler, Robert R. and Strömberg, Jarl-Ove}, + month = nov, + year = {1989}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/00364827.1989.10413424}, + pages = {145--159}, +} + +@article{dauvin_suprabenthic_1996, + title = {Suprabenthic crustacean fauna of a dense {Ampelisca} community from the {English} {Channel}}, + volume = {76}, + issn = {1469-7769, 0025-3154}, + url = {https://www.cambridge.org/core/journals/journal-of-the-marine-biological-association-of-the-united-kingdom/article/abs/suprabenthic-crustacean-fauna-of-a-dense-ampelisca-community-from-the-english-channel/979C0CE4D1ECDBE1E0266849318D1BB1}, + doi = {10.1017/S0025315400040881}, + abstract = {Ninety-six species (97, 677 individuals) were collected over the course of 6 h in five suprabenthic sledge hauls from a very dense Ampelisca fine sand community from the Bay of Morlaix (western English Channel). All the species migrated into the water column at night (98\% of the specimens collected in the suprabenthos were found in the night hauls). The 23 most abundant species collected were classified into five groups based on their height within the water column, but two groups predominated: the upper suprabenthic species, abundant at 0–80–145 m above the sea-bed; and the lower suprabenthic species which were abundant only near the sea bottom (-0–1–0–75 m high). Three different patterns of nocturnal vertical migration were distinguished based on the timing of maximum swimming activity: at dusk; at the beginning of the night; or later in the night. Sexually dimorphic patterns of free-swimming behaviour was observed in Ampelisca and some other species of Amphipoda (Bathyporeia teniupes, Metaphoxusfultoni), and Cumacea (Bodotria pulchella, Pseudocuma longicornis), with many more males than females migrating into the water column at night. Finally, the density of suprabenthic crustaceans in nocturnal hauls was amongst the highest reported from infralittoral or circalittoral suprabenthic studies on other parts of the Atlantic Ocean sampled during spring.}, + language = {en}, + number = {4}, + urldate = {2024-04-26}, + journal = {Journal of the Marine Biological Association of the United Kingdom}, + author = {Dauvin, Jean-Claude and Zouhiri, Souaad}, + month = nov, + year = {1996}, + pages = {909--929}, +} + +@article{rex_community_1981, + title = {Community {Structure} in the {Deep}-{Sea} {Benthos}}, + volume = {12}, + issn = {1543-592X, 1545-2069}, + url = {https://www.annualreviews.org/content/journals/10.1146/annurev.es.12.110181.001555}, + doi = {10.1146/annurev.es.12.110181.001555}, + language = {fr}, + number = {Volume 12,}, + urldate = {2024-04-26}, + journal = {Annual Review of Ecology, Evolution, and Systematics}, + author = {Rex, M. A.}, + month = nov, + year = {1981}, + note = {Publisher: Annual Reviews}, + pages = {331--353}, +} + +@article{wiemers_does_2007, + title = {Does the {DNA} barcoding gap exist? – a case study in blue butterflies ({Lepidoptera}: {Lycaenidae})}, + volume = {4}, + issn = {1742-9994}, + shorttitle = {Does the {DNA} barcoding gap exist?}, + url = {https://doi.org/10.1186/1742-9994-4-8}, + doi = {10.1186/1742-9994-4-8}, + abstract = {DNA barcoding, i.e. the use of a 648 bp section of the mitochondrial gene cytochrome c oxidase I, has recently been promoted as useful for the rapid identification and discovery of species. Its success is dependent either on the strength of the claim that interspecific variation exceeds intraspecific variation by one order of magnitude, thus establishing a "barcoding gap", or on the reciprocal monophyly of species.}, + number = {1}, + urldate = {2024-04-26}, + journal = {Frontiers in Zoology}, + author = {Wiemers, Martin and Fiedler, Konrad}, + month = mar, + year = {2007}, + keywords = {Allopatric Population, Barcoding Approach, Cryptic Species, Incomplete Lineage Sorting, Reciprocal Monophyly}, + pages = {8}, +} + +@article{wilson_speciation_1987, + title = {{SPECIATION} {IN} {THE} {DEEP} {SEA}}, + volume = {18}, + issn = {1543-592X, 1545-2069}, + url = {https://www.annualreviews.org/content/journals/10.1146/annurev.es.18.110187.001153}, + doi = {10.1146/annurev.es.18.110187.001153}, + language = {fr}, + number = {Volume 18, 1987}, + urldate = {2024-04-26}, + journal = {Annual Review of Ecology, Evolution, and Systematics}, + author = {Wilson, George D. F. and Hessler, Robert R.}, + month = nov, + year = {1987}, + note = {Publisher: Annual Reviews}, + pages = {185--207}, +} + +@misc{watling_world_2024-1, + title = {World {Cumacea} {Database}. {Accessed} at https://www.marinespecies.org/cumacea on yyyy-mm-dd}, + copyright = {Creative Commons Attribution 4.0 International}, + shorttitle = {World {Cumacea} {Database}. {Accessed} at https}, + url = {https://www.marinespecies.org/imis.php?dasid=544&doiid=354}, + doi = {10.14284/354}, + abstract = {A world checklist of Cumacea, compiled by taxonomic experts and based on peer-reviewed literature.}, + language = {en}, + urldate = {2024-04-26}, + publisher = {[object Object]}, + author = {Watling, Les and Gerken, Sarah}, + collaborator = {Gerken, Sarah and Watling, Les and {Flanders Marine Institute (VLIZ), Belgium}}, + year = {2024}, + keywords = {Biology, Biology \> Ecology - biodiversity, Biology \> Invertebrates, Cumacea}, + annote = {Other +Cumaceans are small crustaceans, generally 1-10mm in size, which occur from tidal to abyssal depths in marine (and brackish) waters throughout the world. They are found in the first few cms of sand or sand/mud substrates; while they may be locally abundant, their distributions are patchy. Cumaceans feed on microorganisms and organic matter and are, in turn, consumed by bottom feeding organisms including a number of fishes. + +These malacostracans are distinguished by a combination of features including a large carapace which covers many thorasic somites, a narrow, long abdomen, a forked tail, and, in many families, a telson. The sexes are conspicuously dimorphic: females lack pleopods (with one exception, of course!) and have a large brood chamber. The carapace is ornamented in many lineages and appendages are generally highly modified. The morphology of cumaceans is sufficiently distinctive that members of the order are easy to recognize.}, +} + +@incollection{vassilenko_arctic_1989, + address = {Boston, MA}, + title = {Arctic {Ocean} {Cumacea}}, + isbn = {978-1-4613-0677-1}, + url = {https://doi.org/10.1007/978-1-4613-0677-1_17}, + abstract = {The order Cumacea belongs to the super-order Peracarida, subclass Malacostraca, class Crustacea, according to the classification of McLaughlin, 1980. The cumaceans are primarily marine bottom-dwelling burrowing crustaceans. They live on argillaceous sands, feed on detritus, and graze on sand grains or are filter feeders. The Cumacea, like all Peracarida, have an epimorphic larval development; eggs are laid and develop in the brood pouch. This stage is followed by the manca stage and a postlarval stage (McLaughlin, 1980).}, + language = {en}, + urldate = {2024-04-26}, + booktitle = {The {Arctic} {Seas}: {Climatology}, {Oceanography}, {Geology}, and {Biology}}, + publisher = {Springer US}, + author = {Vassilenko, S. V.}, + editor = {Herman, Yvonne}, + year = {1989}, + doi = {10.1007/978-1-4613-0677-1_17}, + pages = {431--444}, +} + +@article{watling_cumacea_2005, + title = {The {Cumacea} of the {Faroe} {Islands} region: water mass relationships and {North} {Atlantic} biogeography}, + volume = {2005}, + journal = {BIOFAR Proceedings}, + author = {Watling, L and Gerken, S}, + year = {2005}, + pages = {137--149}, +} + +@article{haye_molecular_2004, + title = {Molecular insights into {Cumacean} family relationships ({Crustacea}, {Cumacea})}, + volume = {30}, + issn = {1055-7903}, + url = {https://www.sciencedirect.com/science/article/pii/S1055790303003105}, + doi = {10.1016/j.ympev.2003.08.003}, + abstract = {Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many “diagnostic” characters are homoplasious.}, + number = {3}, + urldate = {2024-04-26}, + journal = {Molecular Phylogenetics and Evolution}, + author = {Haye, Pilar A. and Kornfield, Irv and Watling, Les}, + month = mar, + year = {2004}, + keywords = {Peracarida, Cumacea, Bayesian inference, COI, Cytochrome oxidase I, Mitochondrial DNA, Molecular phylogeny}, + pages = {798--809}, +} + +@article{watling_biogeographic_2009, + series = {Marine {Benthic} {Ecology} and {Biodiversity}: {A} {Compilation} of {Recent} {Advances} in {Honor} of {J}. {Frederick} {Grassle}}, + title = {Biogeographic provinces in the {Atlantic} deep sea determined from cumacean distribution patterns}, + volume = {56}, + issn = {0967-0645}, + url = {https://www.sciencedirect.com/science/article/pii/S0967064509001842}, + doi = {10.1016/j.dsr2.2009.05.019}, + abstract = {Cumacean species abundance and presence–absence data were compiled from samples taken along the US northeast slope and rise, from around the Faroe Islands, and from deep-sea transects throughout the Atlantic Ocean. These data were analyzed using hierarchical cluster techniques, the results being used to help determine the boundaries of zoogeographic units in the deep sea. Comparing the results of these analyses with previous studies on protobranchs, tunicates, and sea stars, supports dividing the deep Atlantic Ocean into the following biogeographic units: (1) Norwegian Basin; (2) North Atlantic Upper Bathyal; (3) West European Basin Northern Bathyal; (4) Lusitanian Bathyal; (5) North American Basin Bathyal; (6) West European Basin Abyssal; (7) North American Basin Abyssal; and (8) Angola, Cape, Brazil, and Argentine Basins occupying the more or less isolated basins of the South Atlantic Ocean. These latter are not well-sampled for most groups but appear to be separated from each other.}, + number = {19}, + urldate = {2024-04-26}, + journal = {Deep Sea Research Part II: Topical Studies in Oceanography}, + author = {Watling, Les}, + month = sep, + year = {2009}, + keywords = {Cumacea, Abyssal, Bathyal, Cluster analysis, North American Basin, West European Basin}, + pages = {1747--1753}, +} + +@article{vassilenko_composition_1996, + title = {Composition and biogeographic structure of the cumacean fauna of the {Northeast} {Water} {Polynya}, {Greenland} ({Crustacea} {Peracarida} {Cumacea})}, + volume = {5}, + issn = {0136-006X}, + journal = {Arthropoda Selecta}, + author = {Vassilenko, SV and Brandt, A}, + year = {1996}, + pages = {27--38}, +} + +@article{watling_biogeographic_2009-1, + series = {Marine {Benthic} {Ecology} and {Biodiversity}: {A} {Compilation} of {Recent} {Advances} in {Honor} of {J}. {Frederick} {Grassle}}, + title = {Biogeographic provinces in the {Atlantic} deep sea determined from cumacean distribution patterns}, + volume = {56}, + issn = {0967-0645}, + url = {https://www.sciencedirect.com/science/article/pii/S0967064509001842}, + doi = {10.1016/j.dsr2.2009.05.019}, + abstract = {Cumacean species abundance and presence–absence data were compiled from samples taken along the US northeast slope and rise, from around the Faroe Islands, and from deep-sea transects throughout the Atlantic Ocean. These data were analyzed using hierarchical cluster techniques, the results being used to help determine the boundaries of zoogeographic units in the deep sea. Comparing the results of these analyses with previous studies on protobranchs, tunicates, and sea stars, supports dividing the deep Atlantic Ocean into the following biogeographic units: (1) Norwegian Basin; (2) North Atlantic Upper Bathyal; (3) West European Basin Northern Bathyal; (4) Lusitanian Bathyal; (5) North American Basin Bathyal; (6) West European Basin Abyssal; (7) North American Basin Abyssal; and (8) Angola, Cape, Brazil, and Argentine Basins occupying the more or less isolated basins of the South Atlantic Ocean. These latter are not well-sampled for most groups but appear to be separated from each other.}, + number = {19}, + urldate = {2024-04-26}, + journal = {Deep Sea Research Part II: Topical Studies in Oceanography}, + author = {Watling, Les}, + month = sep, + year = {2009}, + keywords = {Cumacea, Abyssal, Bathyal, Cluster analysis, North American Basin, West European Basin}, + pages = {1747--1753}, +} + +@article{gerken_cumacea_1999, + title = {Cumacea ({Crustacea}) of the {Faroe} {Island} {Region}: {Cumacea} ({Crustacea}) í føroyskum øki}, + issn = {2445-6144}, + journal = {Fróðskaparrit-Faroese Scientific Journal}, + author = {Gerken, Sarah and Watling, Les}, + year = {1999}, + pages = {199--227}, +} + +@article{michael_a_rex_global_2006, + title = {Global bathymetric patterns of standing stock and body size in the deep-sea benthos}, + volume = {317}, + url = {https://www.int-res.com/abstracts/meps/v317/p1-8/}, + abstract = {ABSTRACT: We present the first global-scale analysis of standing stock (abundance and biomass) for 4 major size classes of deep-sea biota: bacteria, metazoan meiofauna, macrofauna and megafauna. The community standing stock decreases with depth; this is a universal phenomenon that involves a complex transition in the relative importance of the different size groups. Bacterial abundance and biomass show no decline with depth. All 3 animal size groups experience significant exponential decreases in both abundance and biomass. The abundance of larger animals is significantly lower and decreases more rapidly than for smaller groups. The resulting drop in average body size with depth confirms Thiel\&\#146;s size-structure hypothesis on very large spatial scales. In terms of their proportion of total community biomass, smaller size classes replace larger size classes. The upper continental slope is dominated by macrofaunal biomass, and the abyss by bacterial and meiofaunal biomass. The dramatic decrease in total community standing stock and the ascendancy of smaller organisms with depth has important implications for deep-sea biodiversity. The bathyal zone (200 to 4000 m) affords more ecological and evolutionary opportunity in the form of energy availability for larger organisms, and consequently supports higher macrofaunal and megafaunal species diversity than the abyss ({\textgreater}4000 m).}, + journal = {Marine Ecology Progress Series}, + author = {{Michael A. Rex} and {Ron J. Etter} and {Jeremy S. Morris} and {Jenifer Crouse} and {Craig R. McClain} and {Nicholas A. Johnson} and {Carol T. Stuart} and {Jody W. Deming} and {Rebecca Thies} and {Renee Avery}}, + year = {2006}, + pages = {1--8}, + annote = {10.3354/meps317001}, +} + +@article{stransky_diversity_2010-1, + title = {Diversity and species composition of peracarids ({Crustacea}: {Malacostraca}) on the {South} {Greenland} shelf: spatial and temporal variation}, + volume = {33}, + issn = {1432-2056}, + shorttitle = {Diversity and species composition of peracarids ({Crustacea}}, + url = {https://doi.org/10.1007/s00300-009-0691-5}, + doi = {10.1007/s00300-009-0691-5}, + abstract = {The interannual variability in peracarid (Crustacea: Malacostraca; Amphipoda, Isopoda, Cumacea, Tanaidacea) species composition and diversity on the South Greenland shelf was studied at four stations over a sampling period of 3 years (2001, 2002 and 2004), using a Rauschert sled at depths of about 160 m. The South Greenland peracarids were relatively stable over the 3 years with respect to evenness and diversity. Moderate changes in temperature and salinity had negligible effects on the species composition, while sediment structure was found to be the most important environmental variable shaping the peracarid fauna.}, + language = {en}, + number = {2}, + urldate = {2024-05-08}, + journal = {Polar Biology}, + author = {Stransky, Bente and Svavarsson, Jörundur}, + month = feb, + year = {2010}, + keywords = {Peracarida, Greenland, Shelf, Spatial and temporal variation, Species distribution}, + pages = {125--139}, +} + +@book{li_host-virus_2023, + title = {Host-{Virus} {Cophylogeny} {Trajectories}: {Investigating} {Molecular} {Relationships} between {Coronaviruses} and {Bat} {Hosts}}, + shorttitle = {Host-{Virus} {Cophylogeny} {Trajectories}}, + abstract = {Background: Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics, host adaptation, and the foundation for disease emergence and spread. In this study, we investigate the cophylogenetic patterns of 69 host-virus connections. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the coevolution between hosts and viruses. +Results: Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two pivotal proteins, ORF1ab and spike, we conduct a comparative analysis of host and coronavirus phylogenies. For ORF1ab, specific window ranges in the multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibit the lowest Robinson and Foulds (RF) distance (i.e. 84.62{\textbackslash}\%), emphasizing their higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) display the lowest RF distance at 88.46{\textbackslash}\%. Our analysis identifies six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. +Conclusions: By employing a multifaceted approach, our comprehensive approach provides a nuanced understanding of the multifaceted interactions governing the coevolutionary dynamics between bat hosts and CoVs. This deeper insight informs our understanding of viral evolution and adaptation mechanisms, illuminating the broader dynamics driving viral diversity.}, + author = {Li, Wanlin and Tahiri, Nadia}, + month = sep, + year = {2023}, + doi = {10.21203/rs.3.rs-3362308/v1}, +} + +@book{koshkarov_phylogeography_2022, + title = {Phylogeography: {Analysis} of genetic and climatic data of {SARS}-{CoV}-2}, + shorttitle = {Phylogeography}, + abstract = {Due to the fact that the SARS-CoV-2 pandemic reaches its peak, researchers around the globe are combining efforts to investigate the genetics of different variants to better deal with its distribution. This paper discusses phylogeographic approaches to examine how patterns of divergence within SARS-CoV-2 coincide with geographic features, such as climatic features. First, we propose a python-based bioinformatic pipeline called aPhylogeo for phylo-geographic analysis written in Python 3 that help researchers better understand the distribution of the virus in specific regions via a configuration file, and then run all the analysis operations in a single run. In particular, the aPhylogeo tool determines which parts of the genetic sequence undergo a high mutation rate depending on geographic conditions, using a sliding window that moves along the genetic sequence alignment in user-defined steps and a window size. As a Python-based cross-platform program, aPhylogeo works on Windows®, MacOS X® and GNU/Linux. The implementation of this pipeline is publicly available on GitHub (https://github.com/tahiri-lab/aPhylogeo). Second, we present an example of analysis of our new aPhylogeo tool on real data (SARS-CoV-2) to understand the occurrence of different variants.}, + author = {Koshkarov, Aleksandr and Li, Wanlin and Luu, My-Linh and Tahiri, Nadia}, + month = jul, + year = {2022}, + doi = {10.25080/majora-212e5952-018}, +} + +@article{li_host-virus_2023-1, + title = {Host-{Virus} {Cophylogeny} {Trajectories}: {Investigating} {Molecular} {Relationships} between {Coronaviruses} and {Bat} {Hosts}}, + author = {Li, Wanlin and Tahiri, Nadia}, + year = {2023}, +} + +@inproceedings{koshkarov_phylogeography_2022-1, + title = {Phylogeography: {Analysis} of genetic and climatic data of {SARS}-{CoV}-2.}, + author = {Koshkarov, Aleksandr and Li, Wanlin and Luu, My-Linh and Tahiri, Nadia}, + year = {2022}, + pages = {159--166}, +} + +@article{li_aphylogeo-covid_2023, + title = {{aPhyloGeo}-{Covid}: {A} web interface for reproducible phylogeographic analysis of {SARS}-{CoV}-2 variation using {Neo4j} and {Snakemake}}, + journal = {NOUVEL ALGORITHME POUR ÉVALUER L’INFLUENCE ENVIRONNEMENTALE DU CORONAVIRUS PAR LE BIAIS D’UNE ANALYSE PHYLOGÉOGRAPHIQUE}, + author = {Li, Wanlin and Tahiri, Nadia}, + year = {2023}, + pages = {44}, +} + +@article{li_aphylogeo-covid_2023-1, + title = {{aPhyloGeo}-{Covid}: {A} web interface for reproducible phylogeographic analysis of {SARS}-{CoV}-2 variation using {Neo4j} and {Snakemake}}, + journal = {NOUVEL ALGORITHME POUR ÉVALUER L’INFLUENCE ENVIRONNEMENTALE DU CORONAVIRUS PAR LE BIAIS D’UNE ANALYSE PHYLOGÉOGRAPHIQUE}, + author = {Li, Wanlin and Tahiri, Nadia}, + year = {2023}, + pages = {44}, +} + +@article{hoffmann_climate_2011, + title = {Climate change and evolutionary adaptation}, + volume = {470}, + issn = {0028-0836}, + number = {7335}, + journal = {Nature}, + author = {Hoffmann, Ary A and Sgrò, Carla M}, + year = {2011}, + note = {Publisher: Nature Publishing Group UK London}, + pages = {479--485}, +} + +@article{ghalambor_adaptive_2007, + title = {Adaptive versus non‐adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments}, + volume = {21}, + issn = {0269-8463}, + number = {3}, + journal = {Functional ecology}, + author = {Ghalambor, Cameron K and McKay, John K and Carroll, Scott P and Reznick, David N}, + year = {2007}, + note = {Publisher: Wiley Online Library}, + pages = {394--407}, +} + +@article{cheviron_genomic_2012, + title = {Genomic insights into adaptation to high-altitude environments}, + volume = {108}, + issn = {1365-2540}, + number = {4}, + journal = {Heredity}, + author = {Cheviron, ZA and Brumfield, RT}, + year = {2012}, + note = {Publisher: Nature Publishing Group}, + pages = {354--361}, +} + +@article{fc_genomic_2012, + title = {The genomic basis of adaptive evolution in threespine sticklebacks}, + volume = {484}, + journal = {Nature}, + author = {Fc, Jones}, + year = {2012}, + pages = {55--61}, +} + +@article{colosimo_widespread_2005, + title = {Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles}, + volume = {307}, + issn = {0036-8075}, + number = {5717}, + journal = {science}, + author = {Colosimo, Pamela F and Hosemann, Kim E and Balabhadra, Sarita and Villarreal Jr, Guadalupe and Dickson, Mark and Grimwood, Jane and Schmutz, Jeremy and Myers, Richard M and Schluter, Dolph and Kingsley, David M}, + year = {2005}, + note = {Publisher: American Association for the Advancement of Science}, + pages = {1928--1933}, +} + +@article{darwin_origin_1968, + title = {On the origin of species by means of natural selection. 1859}, + journal = {London: Murray Google Scholar}, + author = {Darwin, Charles}, + year = {1968}, +} + +@article{darwin_origin_1859, + title = {On the origin of species: facsimile of the first edition}, + author = {Darwin, Charles}, + year = {1859}, + note = {Publisher: LONDON: JOHN MURRAY, ALBEMARLE STREET.}, +} + +@article{barrett_molecular_2011, + title = {Molecular spandrels: tests of adaptation at the genetic level}, + volume = {12}, + issn = {1471-0056}, + number = {11}, + journal = {Nature Reviews Genetics}, + author = {Barrett, Rowan DH and Hoekstra, Hopi E}, + year = {2011}, + note = {Publisher: Nature Publishing Group UK London}, + pages = {767--780}, +} + +@inproceedings{linnen_measuring_2009, + title = {Measuring natural selection on genotypes and phenotypes in the wild}, + volume = {74}, + isbn = {0091-7451}, + publisher = {Cold Spring Harbor Laboratory Press}, + author = {Linnen, Catherine R and Hoekstra, Hopi E}, + year = {2009}, + pages = {155--168}, +} + +@article{fc_genomic_2012-1, + title = {The genomic basis of adaptive evolution in threespine sticklebacks}, + volume = {484}, + journal = {Nature}, + author = {Fc, Jones}, + year = {2012}, + pages = {55--61}, +} + +@article{schluter_evidence_2009, + title = {Evidence for ecological speciation and its alternative}, + volume = {323}, + issn = {0036-8075}, + number = {5915}, + journal = {Science}, + author = {Schluter, Dolph}, + year = {2009}, + note = {Publisher: American Association for the Advancement of Science}, + pages = {737--741}, +} + +@article{ghalambor_adaptive_2007-1, + title = {Adaptive versus non‐adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments}, + volume = {21}, + issn = {0269-8463}, + number = {3}, + journal = {Functional ecology}, + author = {Ghalambor, Cameron K and McKay, John K and Carroll, Scott P and Reznick, David N}, + year = {2007}, + note = {Publisher: Wiley Online Library}, + pages = {394--407}, +} + +@book{frankham_introduction_2002, + title = {Introduction to conservation genetics}, + isbn = {0-521-63985-9}, + publisher = {Cambridge university press}, + author = {Frankham, Richard and Briscoe, David A and Ballou, Jonathan D}, + year = {2002}, +} + +@article{tallmon_alluring_2004, + title = {The alluring simplicity and complex reality of genetic rescue}, + volume = {19}, + issn = {0169-5347}, + number = {9}, + journal = {Trends in ecology \& evolution}, + author = {Tallmon, David A and Luikart, Gordon and Waples, Robin S}, + year = {2004}, + note = {Publisher: Elsevier}, + pages = {489--496}, +} + +@article{reed_correlation_2003, + title = {Correlation between fitness and genetic diversity}, + volume = {17}, + issn = {0888-8892}, + number = {1}, + journal = {Conservation biology}, + author = {Reed, David H and Frankham, Richard}, + year = {2003}, + note = {Publisher: Wiley Online Library}, + pages = {230--237}, +} + +@article{holderegger_brief_2006, + title = {A brief guide to landscape genetics}, + volume = {21}, + number = {6}, + journal = {Landscape ecology}, + author = {Holderegger, Rolf and Wagner, Helene}, + year = {2006}, + note = {Publisher: Kluwer Academic Publishers}, + pages = {793--796}, +} + +@article{balkenhol_identifying_2009, + title = {Identifying future research needs in landscape genetics: where to from here?}, + volume = {24}, + issn = {0921-2973}, + journal = {Landscape Ecology}, + author = {Balkenhol, Niko and Gugerli, Felix and Cushman, Sam A and Waits, Lisette P and Coulon, Aurélie and Arntzen, JW and Holderegger, Rolf and Wagner, Helene H and {Participants of the Landscape Genetics Research Agenda Workshop 2007}}, + year = {2009}, + note = {Publisher: Springer}, + pages = {455--463}, +} + +@article{manel_perspectives_2010, + title = {Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field}, + volume = {19}, + issn = {0962-1083}, + number = {17}, + journal = {Molecular Ecology}, + author = {Manel, Stéphanie and Joost, Stéphane and Epperson, Bryan K and Holderegger, Rolf and Storfer, Andrew and Rosenberg, Michael S and Scribner, Kim T and Bonin, Aurélie and FORTIN, MARIE‐JOSÉE}, + year = {2010}, + note = {Publisher: Wiley Online Library}, + pages = {3760--3772}, +} + +@article{balkenhol_identifying_2009-1, + title = {Identifying future research needs in landscape genetics: where to from here?}, + volume = {24}, + issn = {0921-2973}, + journal = {Landscape Ecology}, + author = {Balkenhol, Niko and Gugerli, Felix and Cushman, Sam A and Waits, Lisette P and Coulon, Aurélie and Arntzen, JW and Holderegger, Rolf and Wagner, Helene H and {Participants of the Landscape Genetics Research Agenda Workshop 2007}}, + year = {2009}, + note = {Publisher: Springer}, + pages = {455--463}, +} + +@article{storfer_putting_2007, + title = {Putting the ‘landscape’in landscape genetics}, + volume = {98}, + issn = {1365-2540}, + number = {3}, + journal = {Heredity}, + author = {Storfer, A and Murphy, MA and Evans, JS and Goldberg, CS and Robinson, S and Spear, SF and Dezzani, R and Delmelle, E and Vierling, L and Waits, LP}, + year = {2007}, + note = {Publisher: Nature Publishing Group}, + pages = {128--142}, +} + +@article{manel_landscape_2003, + title = {Landscape genetics: combining landscape ecology and population genetics}, + volume = {18}, + issn = {0169-5347}, + number = {4}, + journal = {Trends in ecology \& evolution}, + author = {Manel, Stéphanie and Schwartz, Michael K and Luikart, Gordon and Taberlet, Pierre}, + year = {2003}, + note = {Publisher: Elsevier}, + pages = {189--197}, +} + +@article{holderegger_brief_2006-1, + title = {A brief guide to landscape genetics}, + volume = {21}, + number = {6}, + journal = {Landscape ecology}, + author = {Holderegger, Rolf and Wagner, Helene}, + year = {2006}, + note = {Publisher: Kluwer Academic Publishers}, + pages = {793--796}, +} + +@article{balkenhol_identifying_2009-2, + title = {Identifying future research needs in landscape genetics: where to from here?}, + volume = {24}, + issn = {0921-2973}, + journal = {Landscape Ecology}, + author = {Balkenhol, Niko and Gugerli, Felix and Cushman, Sam A and Waits, Lisette P and Coulon, Aurélie and Arntzen, JW and Holderegger, Rolf and Wagner, Helene H and {Participants of the Landscape Genetics Research Agenda Workshop 2007}}, + year = {2009}, + note = {Publisher: Springer}, + pages = {455--463}, +} + +@article{manel_perspectives_2010-1, + title = {Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field}, + volume = {19}, + issn = {0962-1083}, + number = {17}, + journal = {Molecular Ecology}, + author = {Manel, Stéphanie and Joost, Stéphane and Epperson, Bryan K and Holderegger, Rolf and Storfer, Andrew and Rosenberg, Michael S and Scribner, Kim T and Bonin, Aurélie and FORTIN, MARIE‐JOSÉE}, + year = {2010}, + note = {Publisher: Wiley Online Library}, + pages = {3760--3772}, +} + +@article{holderegger_brief_2006-2, + title = {A brief guide to landscape genetics}, + volume = {21}, + number = {6}, + journal = {Landscape ecology}, + author = {Holderegger, Rolf and Wagner, Helene}, + year = {2006}, + note = {Publisher: Kluwer Academic Publishers}, + pages = {793--796}, +} + +@article{balkenhol_landscape_2019, + title = {Landscape genomics: understanding relationships between environmental heterogeneity and genomic characteristics of populations}, + issn = {3030045870}, + journal = {Population genomics: Concepts, approaches and applications}, + author = {Balkenhol, Niko and Dudaniec, Rachael Y and Krutovsky, Konstantin V and Johnson, Jeremy S and Cairns, David M and Segelbacher, Gernot and Selkoe, Kimberly A and von der Heyden, Sophie and Wang, Ian J and Selmoni, Oliver}, + year = {2019}, + note = {Publisher: Springer}, + pages = {261--322}, +} + +@article{luikart_power_2003, + title = {The power and promise of population genomics: from genotyping to genome typing}, + volume = {4}, + issn = {1471-0056}, + number = {12}, + journal = {Nature reviews genetics}, + author = {Luikart, Gordon and England, Phillip R and Tallmon, David and Jordan, Steve and Taberlet, Pierre}, + year = {2003}, + note = {Publisher: Nature Publishing Group UK London}, + pages = {981--994}, +} + +@article{balkenhol_landscape_2019-1, + title = {Landscape genomics: understanding relationships between environmental heterogeneity and genomic characteristics of populations}, + issn = {3030045870}, + journal = {Population genomics: Concepts, approaches and applications}, + author = {Balkenhol, Niko and Dudaniec, Rachael Y and Krutovsky, Konstantin V and Johnson, Jeremy S and Cairns, David M and Segelbacher, Gernot and Selkoe, Kimberly A and von der Heyden, Sophie and Wang, Ian J and Selmoni, Oliver}, + year = {2019}, + note = {Publisher: Springer}, + pages = {261--322}, +} + +@article{shafer_widespread_2013, + title = {Widespread evidence for incipient ecological speciation: a meta‐analysis of isolation‐by‐ecology}, + volume = {16}, + issn = {1461-023X}, + number = {7}, + journal = {Ecology letters}, + author = {Shafer, Aaron BA and Wolf, Jochen BW}, + year = {2013}, + note = {Publisher: Wiley Online Library}, + pages = {940--950}, +} + +@article{manel_perspectives_2010-2, + title = {Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field}, + volume = {19}, + issn = {0962-1083}, + number = {17}, + journal = {Molecular Ecology}, + author = {Manel, Stéphanie and Joost, Stéphane and Epperson, Bryan K and Holderegger, Rolf and Storfer, Andrew and Rosenberg, Michael S and Scribner, Kim T and Bonin, Aurélie and FORTIN, MARIE‐JOSÉE}, + year = {2010}, + note = {Publisher: Wiley Online Library}, + pages = {3760--3772}, +} + +@article{storfer_putting_2007-1, + title = {Putting the ‘landscape’in landscape genetics}, + volume = {98}, + issn = {1365-2540}, + number = {3}, + journal = {Heredity}, + author = {Storfer, A and Murphy, MA and Evans, JS and Goldberg, CS and Robinson, S and Spear, SF and Dezzani, R and Delmelle, E and Vierling, L and Waits, LP}, + year = {2007}, + note = {Publisher: Nature Publishing Group}, + pages = {128--142}, +} +@article{robinson_comparison_1981, + title = {Comparison of phylogenetic trees}, + volume = {53}, + issn = {0025-5564}, + url = {https://www.sciencedirect.com/science/article/pii/0025556481900432}, + doi = {10.1016/0025-5564(81)90043-2}, + abstract = {A metric on general phylogenetic trees is presented. This extends the work of most previous authors, who constructed metrics for binary trees. The metric presented in this paper makes possible the comparison of the many nonbinary phylogenetic trees appearing in the literature. This provides an objective procedure for comparing the different methods for constructing phylogenetic trees. The metric is based on elementary operations which transform one tree into another. Various results obtained in applying these operations are given. They enable the distance between any pair of trees to be calculated efficiently. This generalizes previous work by Bourque to the case where interior vertices can be labeled, and labels may contain more than one element or may be empty.}, + number = {1}, + urldate = {2024-05-26}, + journal = {Mathematical Biosciences}, + author = {Robinson, D. F. and Foulds, L. R.}, + month = feb, + year = {1981}, + pages = {131--147}, +} diff --git a/papers/Gagnon_Keke_Tahiri_2024/myst.yml b/papers/Gagnon_Keke_Tahiri_2024/myst.yml new file mode 100644 index 0000000000..759d228007 --- /dev/null +++ b/papers/Gagnon_Keke_Tahiri_2024/myst.yml @@ -0,0 +1,54 @@ +version: 1 +project: + # Update this to match `scipy-2024-` the folder should be `` + id: scipy-2024-00_tex_template + title: Phylogeographic analysis of the impact of climatic and geographical parameters on the genetic structuring of cumacea in the northern waters of the north atlantic + subtitle: LaTeX edition + # Authors should have affiliations, emails and ORCIDs if available + authors: + - name: Justin Gagnon + email: Justin.Gagnon2@USherbrooke.ca + affiliations: + - Department of Computer Science, University of Sherbrooke, 2500, boul. de l'Université, Sherbrooke, Quebec, J1K 2R1 Canada + - name: Mansour Kebe + email: Mansour.Kebe@USherbrooke.ca + affiliations: + - Department of Computer Science, University of Sherbrooke, 2500, boul. de l'Université, Sherbrooke, Quebec, J1K 2R1 Canada + - name: Nadia Tahiri + email: Nadia.Tahiri@USherbrooke.ca + orcid: 0000-0002-1818-208X + affiliations: + - Department of Computer Science, University of Sherbrooke, 2500, boul. de l'Université, Sherbrooke, Quebec, J1K 2R1 Canada + corresponding: true + keywords: + - Atlantic + - Arctic + - Bioinformatics + - Biology + - Cumacea + - Iceland + - Phylogeny + - Phylogeography + # Add the abbreviations that you use in your paper here + abbreviations: + MyST: Markedly Structured Text + # It is possible to explicitly ignore the `doi-exists` check for certain citation keys + error_rules: + - rule: doi-exists + severity: ignore + keys: + - Atr03 + - terradesert + - jupyter + - sklearn1 + - sklearn2 + # A banner will be generated for you on publication, this is a placeholder + banner: banner.png + # The rest of the information shouldn't be modified + subject: Research Article + open_access: true + license: CC-BY-4.0 + venue: Scipy 2024 + date: 2024-07-10 +site: + template: article-theme diff --git a/presentations/lightning/example/.JOSE-lightning-talk.pdf.icloud b/presentations/lightning/example/.JOSE-lightning-talk.pdf.icloud new file mode 100644 index 0000000000..c34b5b52d1 Binary files /dev/null and b/presentations/lightning/example/.JOSE-lightning-talk.pdf.icloud differ diff --git a/presentations/lightning/example/JOSE-lightning-talk.pdf b/presentations/lightning/example/JOSE-lightning-talk.pdf deleted file mode 100644 index b19aa50a3f..0000000000 Binary files a/presentations/lightning/example/JOSE-lightning-talk.pdf and /dev/null differ